vignettes/echoannot.Rmd
echoannot.RmdTo get the full dataset of all fine-mapped Parkinson’s Disease loci, you can use the following function:
merged_DT <- echodata::get_Nalls2019_merged()Annotate SNP-wise fine-mapping results.
Here, we’re only annotating a small number of SNPs high-confidence
causal SNPs for demo purposes. The more SNPs you supply to
annotate_snps, the longer it will take to query the
selected databases for each SNP.
#### Only query high-confidence fine-mapping SNPs from one locus ####
dat <- merged_DT[Locus=="LRRK2" & Consensus_SNP==TRUE,]
#### Query annotations ####
dat_annot <- echoannot::annotate_snps(dat = dat,
haploreg_annotation = TRUE,
regulomeDB_annotation = TRUE,
biomart_annotation = TRUE)
knitr::kable(dat_annot)
gg_cs_bin <- echoannot::CS_bin_plot(merged_DT = merged_DT,
show_plot = FALSE)
gg_cs_counts <- echoannot::CS_counts_plot(merged_DT = merged_DT,
show_plot = FALSE)
gg_epi <- echoannot::peak_overlap_plot(
merged_DT = merged_DT,
include.NOTT2019_enhancers_promoters = TRUE,
include.NOTT2019_PLACseq = TRUE,
#### Omit many annotations to save time ####
include.NOTT2019_peaks = FALSE,
include.CORCES2020_scATACpeaks = FALSE,
include.CORCES2020_Cicero_coaccess = FALSE,
include.CORCES2020_bulkATACpeaks = FALSE,
include.CORCES2020_HiChIP_FitHiChIP_coaccess = FALSE,
include.CORCES2020_gene_annotations = FALSE)Creates one big merged plot using the subfunctions above.
super_plot <- echoannot::super_summary_plot(merged_DT = merged_DT,
plot_missense = FALSE)
utils::sessionInfo()## R Under development (unstable) (2026-03-12 r89607)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
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## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
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## locale:
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## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: UTC
## tzcode source: system (glibc)
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## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
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## other attached packages:
## [1] echoannot_1.0.1 BiocStyle_2.39.0
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## loaded via a namespace (and not attached):
## [1] aws.s3_0.3.22 BiocIO_1.21.0
## [3] bitops_1.0-9 filelock_1.0.3
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## [7] cellranger_1.1.0 basilisk.utils_1.23.1
## [9] graph_1.89.1 XML_3.99-0.22
## [11] rpart_4.1.24 lifecycle_1.0.5
## [13] OrganismDbi_1.53.2 ensembldb_2.35.0
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