SNP_LOC_DATA.rda

This file is used by MAGMA_Celltyping R package and is too large to store in github <br><br> tmpF1 = tempfile() tmpF2 = tempfile()<br> download.file("https://ctg.cncr.nl/software/MAGMA/ref_data/g1000_eur.zip",tmpF1)<br> library(R.utils)<br> unzip(tmpF1,exdir=dirname(tmpF1)) <br> library(data.table)<br> snpsALL = data.table::fread(sprintf("%s/g1000_eur.bim",dirname(tmpF1)))<br> g1000_snps = as.character(snpsALL$V2)<br> <br> #tmpF1 = tempfile()<br> #tmpF2 = tempfile()<br> #download.file("https://data.broadinstitute.org/alkesgroup/LDSCORE/w_hm3.snplist.bz2",tmpF1)<br> #library(R.utils)<br> #gunzip(tmpF1,tmpF2)<br> #whm3 = read.table(tmpF2,stringsAsFactors = FALSE)<br> #hm3_rsids = whm3[,1]<br> <br> # Get GRCh37 locations<br> #source("https://bioconductor.org/biocLite.R")<br> #BiocManager::install("SNPlocs.Hsapiens.dbSNP144.GRCh37")<br> library("SNPlocs.Hsapiens.dbSNP144.GRCh37")<br> snps #g1000_snps = g1000_snps[grep("^rs",g1000_snps)]<br> snp_locs = snpsById(snps, g1000_snps,ifnotfound="drop")<br> SNP = mcols(snp_locs)$RefSNP_id<br> CHR = as.character(seqnames(snp_locs)) #seqnames(snp_locs)<br> BP = pos(snp_locs)<br> SNP_DATA_GRCh37 = data.frame(SNP=SNP,CHR=CHR,BP=BP,Build="GRCh37",stringsAsFactors=FALSE)<br> #SNP_DATA_GRCh37 = data.table(SNP=SNP,CHR=CHR,BP=BP,Build="GRCh37")<br> #usethis::use_data(SNP_DATA_GRCh37,overwrite = TRUE)<br> <br> # Get GRCh38 locations<br> #source("https://bioconductor.org/biocLite.R")<br> #BiocManager::install("SNPlocs.Hsapiens.dbSNP144.GRCh38")<br> library(SNPlocs.Hsapiens.dbSNP144.GRCh38)<br> snps snp_locs = snpsById(snps, g1000_snps,ifnotfound="drop")<br> SNP = mcols(snp_locs)$RefSNP_id<br> CHR = as.character(seqnames(snp_locs))<br> BP = pos(snp_locs)<br> SNP_DATA_GRCh38 = data.frame(SNP=SNP,CHR=CHR,BP=BP,Build="GRCh38",stringsAsFactors=FALSE)<br> #usethis::use_data(SNP_DATA_GRCh38,overwrite = TRUE)<br> <br> # Save to package /data/<br> SNP_LOC_DATA = rbind(SNP_DATA_GRCh37,SNP_DATA_GRCh38)<br> usethis::use_data(SNP_LOC_DATA,overwrite = TRUE)