Fine Mapping:
Parkinson’s Disease
Fine Mapping:
Parkinson’s Disease
Brian M. Schilder, Bioinformatician II
Raj Lab
Department of Neuroscience
Icahn School of Medicine at Mount Sinai
NYC, New York
RAJ LAB 
Brian M. Schilder, Bioinformatician II
Raj Lab
Department of Neuroscience
Icahn School of Medicine at Mount Sinai
NYC, New York
RAJ LAB
Most Recent Update:
2019-08-23
# knitr::opts_chunk$set(error = T) # Knit even with errors
# devtools::install_local("echolocatoR/", force = T)
# library("echolocatoR")
source("echolocatoR/R/MAIN.R")
# MINERVA PATHS TO SUMMARY STATISTICS DATASETS:
# Data_dirs <- read.csv("./Data/directories_table.csv")
finemap_results <- list()
coloc_results <- list()Nalls et. al. (2019) w/ 23andMe
Statistical Fine-mapping
Parkinson’s Disease GWAS.
# fig.show='hold'
dataset_name <- "Nalls23andMe_2019"
top_SNPs <- Nalls_top_SNPs <- import_topSNPs(
topSS_path = Directory_info(dataset_name, "topSumStats"),
chrom_col = "CHR", position_col = "BP", snp_col="SNP",
pval_col="P, all studies", effect_col="Beta, all studies", gene_col="Nearest Gene",
caption= "Nalls et al. (2018) w/ 23andMe PD GWAS Summary Stats",
group_by_locus = T,
locus_col = "Locus Number",
remove_variants = "rs34637584")
# Manually add new SNP of interest
top_SNPs <- data.table::rbindlist(list(top_SNPs,
data.table::data.table(CHR=14,POS=55360203, SNP="rs3783642",
P=0, Effect=1, Gene="ATG14", Locus=NA ),
data.table::data.table(CHR=12,POS=53797236, SNP="rs34656641",
P=0, Effect=1, Gene="SP1", Locus=NA ),
data.table::data.table(CHR=5,POS=126181862, SNP="rs959573",
P=0, Effect=1, Gene="LMNB1", Locus=NA ),
data.table::data.table(CHR=17,POS=40609405, SNP="rs9897702",
P=0, Effect=1, Gene="ATP6V0A1", Locus=NA )
), use.names = T)
gene_list <- unique(top_SNPs$Gene)
finemap_results[[dataset_name]] <- finemap_gene_list(top_SNPs,
gene_list = unique(c("LRRK2", gene_list)), #
trim_gene_limits = c(T, rep(F,length(gene_list))),
dataset_name = dataset_name,
dataset_type = "GWAS",
query_by ="coordinates",
subset_path = "auto",
finemap_methods = c("SUSIE","FINEMAP"),
#,"ABF","COJO"),
force_new_LD = F,
#,"ABF","FINEMAP","COJO"),
force_new_subset = F,
force_new_finemap = F,
# file_path = Directory_info(dataset_name, "fullSumStats"),
fullSS_path = "./Data/GWAS/Nalls23andMe_2019/nallsEtAl2019_allSamples_allVariants.mod.txt",
chrom_col = "CHR", position_col = "POS", snp_col = "RSID",
pval_col = "p", effect_col = "beta", stderr_col = "se",
freq_col = "freq", MAF_col = "calculate",
A1_col = "A1",
A2_col = "A2",
bp_distance = 500000*2,
download_reference = T,
LD_reference = "1KG_Phase1",
superpopulation = "EUR",
LD_block = F,
min_MAF = 0,
remove_variants = c("rs34637584"),
remove_correlates = c("rs34637584"),
conditioned_snps = "auto", # Use the lead SNP for each gene
n_causal = 10,
plot_types = c("simple"), #"fancy"
remove_tmps = F)## ^^^^^^^^^ Running echolocatoR on: LRRK2 ^^^^^^^^^LRRK2
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Subset file already exists. Importing Data/GWAS/Nalls23andMe_2019/LRRK2/LRRK2_Nalls23andMe_2019_subset.txt …” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/LRRK2/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 560 x 560” [1] “Extracting LD subset for lead SNP: rs76904798” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 560 x 560” [1] “Extracting LD subset for lead SNP: rs76904798” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 560 x 560” [1] “Extracting LD subset for lead SNP: rs76904798” [1] “+ Constructing SNP labels…”
## Warning: Removed 1 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_smooth).[1] “Generating summary table…” [1] “LRRK2 fine-mapped in 5.74 seconds”
## ^^^^^^^^^ Running echolocatoR on: KRTCAP2 ^^^^^^^^^KRTCAP2
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Subset file already exists. Importing Data/GWAS/Nalls23andMe_2019/KRTCAP2/KRTCAP2_Nalls23andMe_2019_subset.txt …” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584” Error in SNP %in% remove_variants : object ‘SNP’ not found Error in eval(e, x, parent.frame()) : object ‘MAF’ not found
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/KRTCAP2/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------Error in SNP %in% unique(row.names(LD_matrix), colnames(LD_matrix)) : object ‘SNP’ not found
## ^^^^^^^^^ Running echolocatoR on: TMEM163 ^^^^^^^^^TMEM163
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/TMEM163/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ TMEM163 Credible Set SNPs”
[1] “Generating summary table…” [1] “TMEM163 fine-mapped in 3.2 seconds”
## ^^^^^^^^^ Running echolocatoR on: STK39 ^^^^^^^^^STK39
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/STK39/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ STK39 Credible Set SNPs”
[1] “Generating summary table…” [1] “STK39 fine-mapped in 6.15 seconds”
## ^^^^^^^^^ Running echolocatoR on: SATB1 ^^^^^^^^^SATB1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/SATB1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ SATB1 Credible Set SNPs”
[1] “Generating summary table…” [1] “SATB1 fine-mapped in 4.93 seconds”
## ^^^^^^^^^ Running echolocatoR on: LINC00693 ^^^^^^^^^LINC00693
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/LINC00693/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 6069 x 6069” [1] “Extracting LD subset for lead SNP: rs6808178” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 6069 x 6069” [1] “Extracting LD subset for lead SNP: rs6808178” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 6069 x 6069” [1] “Extracting LD subset for lead SNP: rs6808178” [1] “+ Constructing SNP labels…”
## Warning: Removed 1 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_smooth).
[1] “+ LINC00693 Credible Set SNPs”
[1] “Generating summary table…” [1] “LINC00693 fine-mapped in 6.65 seconds”
## ^^^^^^^^^ Running echolocatoR on: IP6K2 ^^^^^^^^^IP6K2
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/IP6K2/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ IP6K2 Credible Set SNPs”
[1] “Generating summary table…” [1] “IP6K2 fine-mapped in 3.67 seconds”
## ^^^^^^^^^ Running echolocatoR on: KPNA1 ^^^^^^^^^KPNA1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/KPNA1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ KPNA1 Credible Set SNPs”
[1] “Generating summary table…” [1] “KPNA1 fine-mapped in 5.52 seconds”
## ^^^^^^^^^ Running echolocatoR on: MED12L ^^^^^^^^^MED12L
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/MED12L/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ MED12L Credible Set SNPs”
[1] “Generating summary table…” [1] “MED12L fine-mapped in 6.48 seconds”
## ^^^^^^^^^ Running echolocatoR on: SPTSSB ^^^^^^^^^SPTSSB
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/SPTSSB/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ SPTSSB Credible Set SNPs”
[1] “Generating summary table…” [1] “SPTSSB fine-mapped in 6.19 seconds”
## ^^^^^^^^^ Running echolocatoR on: MCCC1 ^^^^^^^^^MCCC1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/MCCC1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.32 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ MCCC1 Credible Set SNPs”
[1] “Generating summary table…” [1] “MCCC1 fine-mapped in 5.39 seconds”
## ^^^^^^^^^ Running echolocatoR on: TMEM175 ^^^^^^^^^TMEM175
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/TMEM175/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ TMEM175 Credible Set SNPs”
[1] “Generating summary table…” [1] “TMEM175 fine-mapped in 6.12 seconds”
## ^^^^^^^^^ Running echolocatoR on: FCGR2A ^^^^^^^^^FCGR2A
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/FCGR2A/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 5857 x 5857” [1] “Extracting LD subset for lead SNP: rs6658353” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 5857 x 5857” [1] “Extracting LD subset for lead SNP: rs6658353” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 5857 x 5857” [1] “Extracting LD subset for lead SNP: rs6658353” [1] “+ Constructing SNP labels…”
## Warning: Removed 1 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_smooth).
[1] “+ FCGR2A Credible Set SNPs”
[1] “Generating summary table…” [1] “FCGR2A fine-mapped in 9.21 seconds”
## ^^^^^^^^^ Running echolocatoR on: BST1 ^^^^^^^^^BST1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/BST1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.02 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ BST1 Credible Set SNPs”
[1] “Generating summary table…” [1] “BST1 fine-mapped in 10.53 seconds”
## ^^^^^^^^^ Running echolocatoR on: LCORL ^^^^^^^^^LCORL
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/LCORL/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ LCORL Credible Set SNPs”
[1] “Generating summary table…” [1] “LCORL fine-mapped in 7.21 seconds”
## ^^^^^^^^^ Running echolocatoR on: FAM47E-STBD1 ^^^^^^^^^FAM47E-STBD1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/FAM47E-STBD1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ FAM47E-STBD1 Credible Set SNPs”
[1] “Generating summary table…” [1] “FAM47E-STBD1 fine-mapped in 6.56 seconds”
## ^^^^^^^^^ Running echolocatoR on: SNCA ^^^^^^^^^SNCA
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/SNCA/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ SNCA Credible Set SNPs”
[1] “Generating summary table…” [1] “SNCA fine-mapped in 6.44 seconds”
## ^^^^^^^^^ Running echolocatoR on: CAMK2D ^^^^^^^^^CAMK2D
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/CAMK2D/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ CAMK2D Credible Set SNPs”
[1] “Generating summary table…” [1] “CAMK2D fine-mapped in 6.21 seconds”
## ^^^^^^^^^ Running echolocatoR on: CLCN3 ^^^^^^^^^CLCN3
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/CLCN3/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ CLCN3 Credible Set SNPs”
[1] “Generating summary table…” [1] “CLCN3 fine-mapped in 6.41 seconds”
## ^^^^^^^^^ Running echolocatoR on: ELOVL7 ^^^^^^^^^ELOVL7
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/ELOVL7/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ ELOVL7 Credible Set SNPs”
[1] “Generating summary table…” [1] “ELOVL7 fine-mapped in 5.02 seconds”
## ^^^^^^^^^ Running echolocatoR on: PAM ^^^^^^^^^PAM
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/PAM/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ PAM Credible Set SNPs”
[1] “Generating summary table…” [1] “PAM fine-mapped in 5.88 seconds”
## ^^^^^^^^^ Running echolocatoR on: C5orf24 ^^^^^^^^^C5orf24
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/C5orf24/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ C5orf24 Credible Set SNPs”
[1] “Generating summary table…” [1] “C5orf24 fine-mapped in 5.1 seconds”
## ^^^^^^^^^ Running echolocatoR on: LOC100131289 ^^^^^^^^^LOC100131289
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/LOC100131289/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ LOC100131289 Credible Set SNPs”
[1] “Generating summary table…” [1] “LOC100131289 fine-mapped in 4.69 seconds”
## ^^^^^^^^^ Running echolocatoR on: VAMP4 ^^^^^^^^^VAMP4
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/VAMP4/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ VAMP4 Credible Set SNPs”
[1] “Generating summary table…” [1] “VAMP4 fine-mapped in 6.09 seconds”
## ^^^^^^^^^ Running echolocatoR on: TRIM40 ^^^^^^^^^TRIM40
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/TRIM40/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 2264 x 2264” [1] “Extracting LD subset for lead SNP:” Error in setnames(x, value) : Can’t assign 2 names to a 1 column data.table
## ^^^^^^^^^ Running echolocatoR on: HLA-DRB5 ^^^^^^^^^HLA-DRB5
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/HLA-DRB5/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 3178 x 3178” [1] “Extracting LD subset for lead SNP: rs112485576” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 3178 x 3178” [1] “Extracting LD subset for lead SNP: rs112485576” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 3178 x 3178” [1] “Extracting LD subset for lead SNP: rs112485576” [1] “+ Constructing SNP labels…”
## Warning: Removed 3 rows containing missing values (geom_smooth).## Warning: Removed 3 rows containing missing values (geom_smooth).
[1] “+ HLA-DRB5 Credible Set SNPs”
[1] “Generating summary table…” [1] “HLA-DRB5 fine-mapped in 4.55 seconds”
## ^^^^^^^^^ Running echolocatoR on: RIMS1 ^^^^^^^^^RIMS1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/RIMS1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ RIMS1 Credible Set SNPs”
[1] “Generating summary table…” [1] “RIMS1 fine-mapped in 7.03 seconds”
## ^^^^^^^^^ Running echolocatoR on: FYN ^^^^^^^^^FYN
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/FYN/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ FYN Credible Set SNPs”
[1] “Generating summary table…” [1] “FYN fine-mapped in 5.71 seconds”
## ^^^^^^^^^ Running echolocatoR on: RPS12 ^^^^^^^^^RPS12
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/RPS12/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ RPS12 Credible Set SNPs”
[1] “Generating summary table…” [1] “RPS12 fine-mapped in 5.77 seconds”
## ^^^^^^^^^ Running echolocatoR on: GPNMB ^^^^^^^^^GPNMB
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/GPNMB/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 66 x 66” [1] “Extracting LD subset for lead SNP: rs199351” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 66 x 66” [1] “Extracting LD subset for lead SNP: rs199351” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 66 x 66” [1] “Extracting LD subset for lead SNP: rs199351” [1] “+ Constructing SNP labels…”
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 2.3277e+07## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 970.81## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.5402e+05## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 2.3277e+07## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 970.81## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.5402e+05## Warning: Removed 34 rows containing missing values (geom_smooth).## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 2.3277e+07## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 970.81## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 4.5402e+05## Warning: Removed 34 rows containing missing values (geom_smooth).
[1] “+ GPNMB Credible Set SNPs”
[1] “Generating summary table…” [1] “GPNMB fine-mapped in 2.67 seconds”
## ^^^^^^^^^ Running echolocatoR on: GS1-124K5.11 ^^^^^^^^^GS1-124K5.11
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/GS1-124K5.11/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ GS1-124K5.11 Credible Set SNPs”
[1] “Generating summary table…” [1] “GS1-124K5.11 fine-mapped in 6.42 seconds”
## ^^^^^^^^^ Running echolocatoR on: CTSB ^^^^^^^^^CTSB
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/CTSB/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 5883 x 5883” [1] “Extracting LD subset for lead SNP: rs1293298” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 5883 x 5883” [1] “Extracting LD subset for lead SNP: rs1293298” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 5883 x 5883” [1] “Extracting LD subset for lead SNP: rs1293298” [1] “+ Constructing SNP labels…”
## Warning: Removed 12 rows containing missing values (geom_smooth).## Warning: Removed 12 rows containing missing values (geom_smooth).
[1] “+ CTSB Credible Set SNPs”
[1] “Generating summary table…” [1] “CTSB fine-mapped in 6.5 seconds”
## ^^^^^^^^^ Running echolocatoR on: FGF20 ^^^^^^^^^FGF20
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/FGF20/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.02 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ FGF20 Credible Set SNPs”
[1] “Generating summary table…” [1] “FGF20 fine-mapped in 12.9 seconds”
## ^^^^^^^^^ Running echolocatoR on: BIN3 ^^^^^^^^^BIN3
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/BIN3/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ BIN3 Credible Set SNPs”
[1] “Generating summary table…” [1] “BIN3 fine-mapped in 9.7 seconds”
## ^^^^^^^^^ Running echolocatoR on: NUCKS1 ^^^^^^^^^NUCKS1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/NUCKS1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ NUCKS1 Credible Set SNPs”
[1] “Generating summary table…” [1] “NUCKS1 fine-mapped in 5.19 seconds”
## ^^^^^^^^^ Running echolocatoR on: FAM49B ^^^^^^^^^FAM49B
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/FAM49B/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ FAM49B Credible Set SNPs”
[1] “Generating summary table…” [1] “FAM49B fine-mapped in 6.52 seconds”
## ^^^^^^^^^ Running echolocatoR on: SH3GL2 ^^^^^^^^^SH3GL2
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/SH3GL2/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ SH3GL2 Credible Set SNPs”
[1] “Generating summary table…” [1] “SH3GL2 fine-mapped in 11.35 seconds”
## ^^^^^^^^^ Running echolocatoR on: UBAP2 ^^^^^^^^^UBAP2
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/UBAP2/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ UBAP2 Credible Set SNPs”
[1] “Generating summary table…” [1] “UBAP2 fine-mapped in 6.34 seconds”
## ^^^^^^^^^ Running echolocatoR on: ITGA8 ^^^^^^^^^ITGA8
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/ITGA8/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ ITGA8 Credible Set SNPs”
[1] “Generating summary table…” [1] “ITGA8 fine-mapped in 9.63 seconds”
## ^^^^^^^^^ Running echolocatoR on: GBF1 ^^^^^^^^^GBF1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/GBF1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ GBF1 Credible Set SNPs”
[1] “Generating summary table…” [1] “GBF1 fine-mapped in 5.16 seconds”
## ^^^^^^^^^ Running echolocatoR on: INPP5F ^^^^^^^^^INPP5F
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/INPP5F/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ INPP5F Credible Set SNPs”
[1] “Generating summary table…” [1] “INPP5F fine-mapped in 6.94 seconds”
## ^^^^^^^^^ Running echolocatoR on: RNF141 ^^^^^^^^^RNF141
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/RNF141/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 6995 x 6995” [1] “Extracting LD subset for lead SNP: rs7938782” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 6995 x 6995” [1] “Extracting LD subset for lead SNP: rs7938782” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 6995 x 6995” [1] “Extracting LD subset for lead SNP: rs7938782” [1] “+ Constructing SNP labels…”
## Warning: Removed 1 rows containing missing values (geom_smooth).## Warning: Removed 1 rows containing missing values (geom_smooth).
[1] “+ RNF141 Credible Set SNPs”
[1] “Generating summary table…” [1] “RNF141 fine-mapped in 9.28 seconds”
## ^^^^^^^^^ Running echolocatoR on: DLG2 ^^^^^^^^^DLG2
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/DLG2/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ DLG2 Credible Set SNPs”
[1] “Generating summary table…” [1] “DLG2 fine-mapped in 5.96 seconds”
## ^^^^^^^^^ Running echolocatoR on: IGSF9B ^^^^^^^^^IGSF9B
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/IGSF9B/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ IGSF9B Credible Set SNPs”
[1] “Generating summary table…” [1] “IGSF9B fine-mapped in 10.02 seconds”
## ^^^^^^^^^ Running echolocatoR on: ITPKB ^^^^^^^^^ITPKB
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/ITPKB/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ ITPKB Credible Set SNPs”
[1] “Generating summary table…” [1] “ITPKB fine-mapped in 5.89 seconds”
## ^^^^^^^^^ Running echolocatoR on: SCAF11 ^^^^^^^^^SCAF11
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/SCAF11/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ SCAF11 Credible Set SNPs”
[1] “Generating summary table…” [1] “SCAF11 fine-mapped in 4.76 seconds”
## ^^^^^^^^^ Running echolocatoR on: HIP1R ^^^^^^^^^HIP1R
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/HIP1R/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ HIP1R Credible Set SNPs”
[1] “Generating summary table…” [1] “HIP1R fine-mapped in 5.68 seconds”
## ^^^^^^^^^ Running echolocatoR on: FBRSL1 ^^^^^^^^^FBRSL1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/FBRSL1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ FBRSL1 Credible Set SNPs”
[1] “Generating summary table…” [1] “FBRSL1 fine-mapped in 6.24 seconds”
## ^^^^^^^^^ Running echolocatoR on: CAB39L ^^^^^^^^^CAB39L
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/CAB39L/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ CAB39L Credible Set SNPs”
[1] “Generating summary table…” [1] “CAB39L fine-mapped in 13.5 seconds”
## ^^^^^^^^^ Running echolocatoR on: MBNL2 ^^^^^^^^^MBNL2
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/MBNL2/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.02 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ MBNL2 Credible Set SNPs”
[1] “Generating summary table…” [1] “MBNL2 fine-mapped in 9.57 seconds”
## ^^^^^^^^^ Running echolocatoR on: MIPOL1 ^^^^^^^^^MIPOL1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/MIPOL1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.08 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 5098 x 5098” [1] “Extracting LD subset for lead SNP: rs12147950” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 5098 x 5098” [1] “Extracting LD subset for lead SNP: rs12147950” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 5098 x 5098” [1] “Extracting LD subset for lead SNP: rs12147950” [1] “+ Constructing SNP labels…”
## Warning: Removed 1 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_smooth).
[1] “+ MIPOL1 Credible Set SNPs”
[1] “Generating summary table…” [1] “MIPOL1 fine-mapped in 7.84 seconds”
## ^^^^^^^^^ Running echolocatoR on: GCH1 ^^^^^^^^^GCH1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/GCH1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.02 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ GCH1 Credible Set SNPs”
[1] “Generating summary table…” [1] “GCH1 fine-mapped in 12.06 seconds”
## ^^^^^^^^^ Running echolocatoR on: RPS6KL1 ^^^^^^^^^RPS6KL1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/RPS6KL1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.03 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ RPS6KL1 Credible Set SNPs”
[1] “Generating summary table…” [1] “RPS6KL1 fine-mapped in 14.86 seconds”
## ^^^^^^^^^ Running echolocatoR on: GALC ^^^^^^^^^GALC
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/GALC/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ GALC Credible Set SNPs”
[1] “Generating summary table…” [1] “GALC fine-mapped in 11.6 seconds”
## ^^^^^^^^^ Running echolocatoR on: VPS13C ^^^^^^^^^VPS13C
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/VPS13C/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ VPS13C Credible Set SNPs”
[1] “Generating summary table…” [1] “VPS13C fine-mapped in 11.79 seconds”
## ^^^^^^^^^ Running echolocatoR on: SIPA1L2 ^^^^^^^^^SIPA1L2
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/SIPA1L2/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ SIPA1L2 Credible Set SNPs”
[1] “Generating summary table…” [1] “SIPA1L2 fine-mapped in 12.41 seconds”
## ^^^^^^^^^ Running echolocatoR on: SYT17 ^^^^^^^^^SYT17
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/SYT17/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ SYT17 Credible Set SNPs”
[1] “Generating summary table…” [1] “SYT17 fine-mapped in 5.6 seconds”
## ^^^^^^^^^ Running echolocatoR on: CD19 ^^^^^^^^^CD19
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/CD19/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 2686 x 2686” [1] “Extracting LD subset for lead SNP: rs2904880” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 2686 x 2686” [1] “Extracting LD subset for lead SNP: rs2904880” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 2686 x 2686” [1] “Extracting LD subset for lead SNP: rs2904880” [1] “+ Constructing SNP labels…”
## Warning: Removed 4 rows containing missing values (geom_smooth).## Warning: Removed 4 rows containing missing values (geom_smooth).
[1] “+ CD19 Credible Set SNPs”
[1] “Generating summary table…” [1] “CD19 fine-mapped in 4.43 seconds”
## ^^^^^^^^^ Running echolocatoR on: SETD1A ^^^^^^^^^SETD1A
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/SETD1A/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ SETD1A Credible Set SNPs”
[1] “Generating summary table…” [1] “SETD1A fine-mapped in 4.89 seconds”
## ^^^^^^^^^ Running echolocatoR on: NOD2 ^^^^^^^^^NOD2
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/NOD2/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ NOD2 Credible Set SNPs”
[1] “Generating summary table…” [1] “NOD2 fine-mapped in 7.31 seconds”
## ^^^^^^^^^ Running echolocatoR on: CASC16 ^^^^^^^^^CASC16
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/CASC16/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 5212 x 5212” [1] “Extracting LD subset for lead SNP: rs3104783” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 5212 x 5212” [1] “Extracting LD subset for lead SNP: rs3104783” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 5212 x 5212” [1] “Extracting LD subset for lead SNP: rs3104783” [1] “+ Constructing SNP labels…”
## Warning: Removed 1 rows containing missing values (geom_smooth).## Warning: Removed 1 rows containing missing values (geom_smooth).
[1] “+ CASC16 Credible Set SNPs”
[1] “Generating summary table…” [1] “CASC16 fine-mapped in 7.1 seconds”
## ^^^^^^^^^ Running echolocatoR on: CHD9 ^^^^^^^^^CHD9
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/CHD9/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ CHD9 Credible Set SNPs”
[1] “Generating summary table…” [1] “CHD9 fine-mapped in 10.81 seconds”
## ^^^^^^^^^ Running echolocatoR on: CHRNB1 ^^^^^^^^^CHRNB1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/CHRNB1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 5567 x 5567” [1] “Extracting LD subset for lead SNP: rs12600861” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 5567 x 5567” [1] “Extracting LD subset for lead SNP: rs12600861” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 5567 x 5567” [1] “Extracting LD subset for lead SNP: rs12600861” [1] “+ Constructing SNP labels…”
## Warning: Removed 1 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_smooth).
[1] “+ CHRNB1 Credible Set SNPs”
[1] “Generating summary table…” [1] “CHRNB1 fine-mapped in 16.81 seconds”
## ^^^^^^^^^ Running echolocatoR on: RETREG3 ^^^^^^^^^RETREG3
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/RETREG3/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ RETREG3 Credible Set SNPs”
[1] “Generating summary table…” [1] “RETREG3 fine-mapped in 5.33 seconds”
## ^^^^^^^^^ Running echolocatoR on: FAM171A2 ^^^^^^^^^FAM171A2
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/FAM171A2/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 4163 x 4163” [1] “Extracting LD subset for lead SNP: rs850738” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 4163 x 4163” [1] “Extracting LD subset for lead SNP: rs850738” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 4163 x 4163” [1] “Extracting LD subset for lead SNP: rs850738” [1] “+ Constructing SNP labels…”
## Warning: Removed 1 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_smooth).
[1] “+ FAM171A2 Credible Set SNPs”
[1] “Generating summary table…” [1] “FAM171A2 fine-mapped in 4.69 seconds”
## ^^^^^^^^^ Running echolocatoR on: CRHR1 ^^^^^^^^^CRHR1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/CRHR1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 1774 x 1774” [1] “Extracting LD subset for lead SNP:” Error in setnames(x, value) : Can’t assign 2 names to a 1 column data.table
## ^^^^^^^^^ Running echolocatoR on: KCNS3 ^^^^^^^^^KCNS3
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/KCNS3/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ KCNS3 Credible Set SNPs”
[1] “Generating summary table…” [1] “KCNS3 fine-mapped in 8.52 seconds”
## ^^^^^^^^^ Running echolocatoR on: WNT3 ^^^^^^^^^WNT3
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/WNT3/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ WNT3 Credible Set SNPs”
[1] “Generating summary table…” [1] “WNT3 fine-mapped in 4.17 seconds”
## ^^^^^^^^^ Running echolocatoR on: BRIP1 ^^^^^^^^^BRIP1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/BRIP1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ BRIP1 Credible Set SNPs”
[1] “Generating summary table…” [1] “BRIP1 fine-mapped in 4.59 seconds”
## ^^^^^^^^^ Running echolocatoR on: DNAH17 ^^^^^^^^^DNAH17
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/DNAH17/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.03 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 7838 x 7838” [1] “Extracting LD subset for lead SNP: rs666463” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 7838 x 7838” [1] “Extracting LD subset for lead SNP: rs666463” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 7838 x 7838” [1] “Extracting LD subset for lead SNP: rs666463” [1] “+ Constructing SNP labels…”
## Warning: Removed 3 rows containing missing values (geom_smooth).## Warning: Removed 3 rows containing missing values (geom_smooth).
[1] “+ DNAH17 Credible Set SNPs”
[1] “Generating summary table…” [1] “DNAH17 fine-mapped in 18.91 seconds”
## ^^^^^^^^^ Running echolocatoR on: ASXL3 ^^^^^^^^^ASXL3
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/ASXL3/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ ASXL3 Credible Set SNPs”
[1] “Generating summary table…” [1] “ASXL3 fine-mapped in 6.41 seconds”
## ^^^^^^^^^ Running echolocatoR on: RIT2 ^^^^^^^^^RIT2
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/RIT2/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ RIT2 Credible Set SNPs”
[1] “Generating summary table…” [1] “RIT2 fine-mapped in 11.7 seconds”
## ^^^^^^^^^ Running echolocatoR on: MEX3C ^^^^^^^^^MEX3C
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/MEX3C/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 5345 x 5345” [1] “Extracting LD subset for lead SNP: rs8087969” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 5345 x 5345” [1] “Extracting LD subset for lead SNP: rs8087969” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 5345 x 5345” [1] “Extracting LD subset for lead SNP: rs8087969” [1] “+ Constructing SNP labels…”
## Warning: Removed 1 rows containing missing values (geom_smooth).## Warning: Removed 1 rows containing missing values (geom_smooth).
[1] “+ MEX3C Credible Set SNPs”
[1] “Generating summary table…” [1] “MEX3C fine-mapped in 10.65 seconds”
## ^^^^^^^^^ Running echolocatoR on: SPPL2B ^^^^^^^^^SPPL2B
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/SPPL2B/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.05 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ SPPL2B Credible Set SNPs”
[1] “Generating summary table…” [1] “SPPL2B fine-mapped in 14.81 seconds”
## ^^^^^^^^^ Running echolocatoR on: CRLS1 ^^^^^^^^^CRLS1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/CRLS1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ CRLS1 Credible Set SNPs”
[1] “Generating summary table…” [1] “CRLS1 fine-mapped in 8.84 seconds”
## ^^^^^^^^^ Running echolocatoR on: DYRK1A ^^^^^^^^^DYRK1A
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/DYRK1A/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 5845 x 5845” [1] “Extracting LD subset for lead SNP: rs2248244” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 5845 x 5845” [1] “Extracting LD subset for lead SNP: rs2248244” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 5845 x 5845” [1] “Extracting LD subset for lead SNP: rs2248244” [1] “+ Constructing SNP labels…”
## Warning: Removed 1 rows containing missing values (geom_smooth).
## Warning: Removed 1 rows containing missing values (geom_smooth).
[1] “+ DYRK1A Credible Set SNPs”
[1] “Generating summary table…” [1] “DYRK1A fine-mapped in 8 seconds”
## ^^^^^^^^^ Running echolocatoR on: KCNIP3 ^^^^^^^^^KCNIP3
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/KCNIP3/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 1269 x 1269” [1] “Extracting LD subset for lead SNP: rs2042477” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 1269 x 1269” [1] “Extracting LD subset for lead SNP: rs2042477” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 1269 x 1269” [1] “Extracting LD subset for lead SNP: rs2042477” [1] “+ Constructing SNP labels…”
## Warning: Removed 3 rows containing missing values (geom_smooth).## Warning: Removed 3 rows containing missing values (geom_smooth).
[1] “+ KCNIP3 Credible Set SNPs”
[1] “Generating summary table…” [1] “KCNIP3 fine-mapped in 4.67 seconds”
## ^^^^^^^^^ Running echolocatoR on: MAP4K4 ^^^^^^^^^MAP4K4
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/MAP4K4/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ MAP4K4 Credible Set SNPs”
[1] “Generating summary table…” [1] “MAP4K4 fine-mapped in 7.87 seconds”
## ^^^^^^^^^ Running echolocatoR on: ATG14 ^^^^^^^^^ATG14
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/ATG14/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.01 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 3571 x 3571” [1] “Extracting LD subset for lead SNP:” Error in setnames(x, value) : Can’t assign 2 names to a 1 column data.table
## ^^^^^^^^^ Running echolocatoR on: SP1 ^^^^^^^^^SP1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/SP1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 68 x 68” [1] “Extracting LD subset for lead SNP: rs34656641” [1] “+ Constructing SNP labels…” [1] “Plotting… SUSIE” [1] “LD Matrix dimensions: 68 x 68” [1] “Extracting LD subset for lead SNP: rs34656641” [1] “+ Constructing SNP labels…” [1] “Plotting… FINEMAP” [1] “LD Matrix dimensions: 68 x 68” [1] “Extracting LD subset for lead SNP: rs34656641” [1] “+ Constructing SNP labels…”
## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 5.3775e+07## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1001.4## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0121e+07## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 5.3775e+07## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1001.4## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0121e+07## Warning: Removed 14 rows containing missing values (geom_smooth).## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : span too small. fewer data values than degrees of freedom.## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : pseudoinverse used at 5.3775e+07## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : neighborhood radius 1001.4## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric =
## parametric, : There are other near singularities as well. 1.0121e+07## Warning: Removed 14 rows containing missing values (geom_smooth).
[1] “+ SP1 Credible Set SNPs”
[1] “Generating summary table…” [1] “SP1 fine-mapped in 4.24 seconds”
## ^^^^^^^^^ Running echolocatoR on: LMNB1 ^^^^^^^^^LMNB1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/LMNB1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0 seconds.”
## --------------- Step 7: Visualize --------------[1] “Plotting… original” [1] “LD Matrix dimensions: 0 x 0” [1] “Extracting LD subset for lead SNP:” Error in x[subset & !is.na(subset), vars, drop = drop] : (subscript) logical subscript too long
## ^^^^^^^^^ Running echolocatoR on: ATP6V0A1 ^^^^^^^^^ATP6V0A1
[1] ""
## ------------------ Step 1: Query ---------------[1] “+ Importing previous Multi-finemap file…Importing summary stats.” [1] “Subset file looks good! :)” [1] “Removing specified variants: rs34637584”
## --- Step 2: Calculate Linkage Disequilibrium ---[1] “+ Previously computed LD matrix detected. Importing… Data/GWAS/Nalls23andMe_2019/ATP6V0A1/plink/LD_matrix.RData”
## -------------- Step 3: Filter SNPs -------------
## -------- Step 4: Statistically Fine-map --------[1] “++ Previously multi-fine-mapped results identified. Importing…” [1] “++ Fine-mapping with ‘SUSIE, FINEMAP’ completed in 0.04 seconds.”
## --------------- Step 7: Visualize --------------
[1] “+ ATP6V0A1 Credible Set SNPs”
[1] “Generating summary table…” [1] “ATP6V0A1 fine-mapped in 10.27 seconds”
Summarize Fine-mapping Results
Gather Annotations
merged_results <- merge_finemapping_results(minimum_support=1,
include_leadSNPs=T,
xlsx_path="./Data/annotated_finemapping_results.xlsx",
from_storage=T,
haploreg_annotation=T,
biomart_annotation=T,
verbose = F)## [1] "++ Submitting chunk 1 / 1"## Note: zip::zip() is deprecated, please use zip::zipr() insteadSession Information
## R version 3.6.1 (2019-07-05)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Mojave 10.14.5
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] biomaRt_2.40.3 BiocManager_1.30.4 tidyr_0.8.3
## [4] gaston_1.5.5 RcppParallel_4.4.3 Rcpp_1.0.2
## [7] curl_4.0 ggrepel_0.8.1 plotly_4.9.0
## [10] ggplot2_3.2.1 dplyr_0.8.3 data.table_1.12.2
## [13] readxl_1.3.1 devtools_2.1.0 usethis_1.5.1
## [16] R.utils_2.9.0 R.oo_1.22.0 R.methodsS3_1.7.1
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-6 fs_1.3.1 haploR_3.0.1
## [4] bit64_0.9-7 progress_1.2.2 httr_1.4.1
## [7] rprojroot_1.3-2 tools_3.6.1 backports_1.1.4
## [10] R6_2.4.0 DT_0.8 DBI_1.0.0
## [13] lazyeval_0.2.2 BiocGenerics_0.30.0 colorspace_1.4-1
## [16] withr_2.1.2 tidyselect_0.2.5 prettyunits_1.0.2
## [19] processx_3.4.1 bit_1.1-14 compiler_3.6.1
## [22] cli_1.1.0 Biobase_2.44.0 desc_1.2.0
## [25] labeling_0.3 scales_1.0.0 callr_3.3.1
## [28] stringr_1.4.0 digest_0.6.20 rmarkdown_1.14
## [31] pkgconfig_2.0.2 htmltools_0.3.6 sessioninfo_1.1.1
## [34] htmlwidgets_1.3 rlang_0.4.0 RSQLite_2.1.2
## [37] shiny_1.3.2 jsonlite_1.6 crosstalk_1.0.0
## [40] zip_2.0.3 RCurl_1.95-4.12 magrittr_1.5
## [43] munsell_0.5.0 S4Vectors_0.22.0 stringi_1.4.3
## [46] yaml_2.2.0 plyr_1.8.4 pkgbuild_1.0.4
## [49] grid_3.6.1 blob_1.2.0 parallel_3.6.1
## [52] promises_1.0.1 crayon_1.3.4 cowplot_1.0.0
## [55] hms_0.5.0 zeallot_0.1.0 knitr_1.24
## [58] ps_1.3.0 pillar_1.4.2 RUnit_0.4.32
## [61] stats4_3.6.1 pkgload_1.0.2 XML_3.98-1.20
## [64] glue_1.3.1 evaluate_0.14 remotes_2.1.0
## [67] vctrs_0.2.0 httpuv_1.5.1 testthat_2.2.1
## [70] cellranger_1.1.0 gtable_0.3.0 purrr_0.3.2
## [73] assertthat_0.2.1 openxlsx_4.1.0.1 xfun_0.8
## [76] mime_0.7 xtable_1.8-4 later_0.8.0
## [79] viridisLite_0.3.0 tibble_2.1.3 AnnotationDbi_1.46.0
## [82] memoise_1.1.0 IRanges_2.18.1## [1] "susieR 0.8.1.521"