inst/data/GenerateData.R

In tshmak/lassosum: LASSO with summary statistics and a reference panel

# Tmisc()
# setwd(attachroot("/WORK/myRpackages/lassosum/inst/data"))
# Tim.load(Rplink)
# set.seed(1000)
# chr22 <- attachroot("~/DATA/1000G/PLINK/chr22")
# chr21 <- attachroot("~/DATA/1000G/PLINK/chr21")
# subsample(bfile=chr21, out="chr21", maf=0.05, fill.missing.a2=T,
#           keep=logical.vector(1:200,2504), p=1000, P=20000, silent=F)
# subsample(bfile=chr22, out="chr22", maf=0.05, fill.missing.a2=T,
#           keep=logical.vector(1:200,2504), p=1000, P=20000, silent=F)
# plink(bfile="chr21", cmd="--bmerge chr22", out="test", silent=F)
# 
# subsample(bfile="test", QC=F, p=1800, out="testsample")
# subsample(bfile="test", QC=F, p=1800, out="refpanel")
# test.fam <- read.table.tim("testsample.fam")
# test.fam$V6 <- rbinom(nrow(test.fam), 1, 0.5)
# write.table.tim(test.fam, file="testsample.fam", col.names=F)
# library(data.table)
# sumstats <- fread(attachroot("/DATA/summarystats/RA/RA_GWASmeta_European_v2.txt"))
# bim <- fread("test.bim")
# m <- matchpos(sumstats,bim, chr="Chr", pos="Position(hg19)", ref.chr = "V1", ref.pos="V4", rm.duplicates = T)
# sumstats.tokeep <- sumstats[m$order]
# colnames(sumstats.tokeep)[c(3,6,7,8,9)] <- c("Position", "OR_A1", "OR_95_CIlow", "OR_95_CIup", "P_val")
# write.table.tim(sumstats.tokeep, file="summarystats.txt")
# # system("cp ~/DATA/ldetect/src/EUR/fourier_ls-all.bed .")
# system("rm chr21.* chr22.* test.* *.log *.nosex")
# 
# #### PHENO and COVAR file ####
# PHENO <- test.fam[sample(nrow(test.fam), 180), c(1,2,6)]
# colnames(PHENO) <- c("FID", "IID", "pheno")
# COVAR <- test.fam[sample(nrow(test.fam), 180), c(1,2)]
# colnames(COVAR) <- c("FID", "IID")
# COVAR <- cbind(COVAR, rnorm(nrow(COVAR)), rnorm(nrow(COVAR)))
# 
# write.table.tim(PHENO, file="testsample.pheno.txt", header = TRUE)
# write.table.tim(COVAR, file="testsample.covar.txt", header = TRUE)