Summary stats of the top SNP(s) per locus. Used to query locus subsets.for fine-mapping.
data("topSNPs_Kunkle2019")An object of class data.table (inherits from data.frame) with 8 rows and 7 columns.
library(dplyr)
path <- file.path("/Volumes/bms20/projects/neurogenomics-lab/live",
"GWAS_sumstats/OpenGWAS/ieu-b-2.tsv.gz")
fullSS <- data.table::fread(path)supp_remote <- file.path(
"https://static-content.springer.com/esm",
"art
"MediaObjects/41588_2019_358_MOESM3_ESM.xlsx")
supp_local <- file.path(tempdir(),basename(supp_remote))
utils::download.file(supp_remote, supp_local)
topSS <- readxl::read_excel(supp_local,
sheet = "Supplementary Table 8",
skip = 2)
dplyr::rename(SNP="Top Associated SNV")
topSS <- merge(topSS,
subset(fullSS, SNP
by="SNP")paths <- googledrive::drive_download(
file.path("https://docs.google.com/spreadsheets/d",
"1BgLQaRZd9L7JoO8IbpzhUCRFdTdLgJvD/edit#gid=236666677"),
overwrite = TRUE)
meta <- readxl::read_excel(paths$local_path, sheet = "GWAS")
meta <- subset(meta, dataset=="Kunkle_2019")topSNPs <- echodata::import_topSNPs(
topSS = topSS,
sheet = meta$top_sheet,
CHR = meta$top_chrom,
POS = meta$top_pos,
SNP = meta$top_snp,
P = "P",
Effect = "BETA",
Locus = meta$top_locus)
topSNPs_Kunkle2019 <- topSNPs
usethis::use_data(topSNPs_Kunkle2019, overwrite=TRUE)