get_Kunkle2019: Example GWAS summary statistics: Kunkle2019

In RajLabMSSM/echodata: echoverse module: Fine-mapping data access and formatting

Example GWAS summary statistics: Kunkle2019

Description

Downsampled GWAS summary statistics from Kunkle et al. 2019 Alzheimer's Disease GWAS.

Usage

get_Kunkle2019()

Source

Kunkle et al. 2019, The Lancet Neurology

# meta <- MungeSumstats::find_sumstats(ids = "ieu_b_2") # Kunkle2019 <- MungeSumstats::import_sumstats(ids = meta$id[1]) path <- file.path("/Volumes/bms20/projects/neurogenomics-lab/live", "GWAS_sumstats/OpenGWAS/ieu-b-2.tsv.gz") Kunkle2019 <- data.table::fread(path) Kunkle2019 <- subset(Kunkle2019, P<5e-8) Kunkle2019 <- extract_loci(topSNPs = echodata::topSNPs_Kunkle2019, fullSS = Kunkle2019) #### piggyback #### tmp <- file.path(tempdir(),"Kunkle2019.tsv.gz") data.table::fwrite(Kunkle2019,tmp,sep="\t") piggyback::pb_upload(file = tmp, repo = "RajLabMSSM/echodata")

RajLabMSSM/echodata documentation built on Nov. 21, 2023, 8 a.m.