SNP_LOC_DATA.rda

This file is used by MAGMA_Celltyping R package and is too large to store in github

tmpF1 = tempfile() tmpF2 = tempfile()
download.file("https://ctg.cncr.nl/software/MAGMA/ref_data/g1000_eur.zip",tmpF1)
library(R.utils)
unzip(tmpF1,exdir=dirname(tmpF1))
library(data.table)
snpsALL = data.table::fread(sprintf("%s/g1000_eur.bim",dirname(tmpF1)))
g1000_snps = as.character(snpsALL$V2)

#tmpF1 = tempfile()
#tmpF2 = tempfile()
#download.file("https://data.broadinstitute.org/alkesgroup/LDSCORE/w_hm3.snplist.bz2",tmpF1)
#library(R.utils)
#gunzip(tmpF1,tmpF2)
#whm3 = read.table(tmpF2,stringsAsFactors = FALSE)
#hm3_rsids = whm3[,1]

# Get GRCh37 locations
#source("https://bioconductor.org/biocLite.R")
#BiocManager::install("SNPlocs.Hsapiens.dbSNP144.GRCh37")
library("SNPlocs.Hsapiens.dbSNP144.GRCh37")
snps <- SNPlocs.Hsapiens.dbSNP144.GRCh37
#g1000_snps = g1000_snps[grep("^rs",g1000_snps)]
snp_locs = snpsById(snps, g1000_snps,ifnotfound="drop")
SNP = mcols(snp_locs)$RefSNP_id
CHR = as.character(seqnames(snp_locs)) #seqnames(snp_locs)
BP = pos(snp_locs)
SNP_DATA_GRCh37 = data.frame(SNP=SNP,CHR=CHR,BP=BP,Build="GRCh37",stringsAsFactors=FALSE)
#SNP_DATA_GRCh37 = data.table(SNP=SNP,CHR=CHR,BP=BP,Build="GRCh37")
#usethis::use_data(SNP_DATA_GRCh37,overwrite = TRUE)

# Get GRCh38 locations
#source("https://bioconductor.org/biocLite.R")
#BiocManager::install("SNPlocs.Hsapiens.dbSNP144.GRCh38")
library(SNPlocs.Hsapiens.dbSNP144.GRCh38)
snps <- SNPlocs.Hsapiens.dbSNP144.GRCh38
snp_locs = snpsById(snps, g1000_snps,ifnotfound="drop")
SNP = mcols(snp_locs)$RefSNP_id
CHR = as.character(seqnames(snp_locs))
BP = pos(snp_locs)
SNP_DATA_GRCh38 = data.frame(SNP=SNP,CHR=CHR,BP=BP,Build="GRCh38",stringsAsFactors=FALSE)
#usethis::use_data(SNP_DATA_GRCh38,overwrite = TRUE)

# Save to package /data/
SNP_LOC_DATA = rbind(SNP_DATA_GRCh37,SNP_DATA_GRCh38)
usethis::use_data(SNP_LOC_DATA,overwrite = TRUE)