我有这个代码,我想要并行,但我似乎无法让它工作。 这个想法是,对于每个值chr,snp_sel(geno_data,k,bl)给我一个k列的矩阵,这些列随后逐个写入文件。 我怎么能在这个循环中%dopar%?
foreach(chr=1:length(chrs_raw)) %dopar%
{
start = Sys.time()
print(start)
print(chr)
# get .raw file name + path
rawfile = paste(RAWfolder, chrs_raw[chr],sep="/")
# get .bim file name + path
bimfile = paste(RAWfolder, chrs_bim[chr],sep="/")
# Read in genetype data in raw format
geno_data = fread(rawfile, data.table=FALSE, showProgress = FALSE)
# Remove first 7 columns
geno_data = as.matrix(geno_data[,c(7:ncol(geno_data))])
# Apply LD subsetting function Lubke et al 2012
LDsubset = snp_sel(geno_data,k, bl)
rm(geno_data)
snp_data = fread(bimfile, data.table=FALSE, showProgress = FALSE)
for(subsets in 1:ncol(LDsubset))
{
dataout = snp_data[LDsubset[,subsets][LDsubset[,subsets] != 0],2]
outfile = paste(gsub(".bim","",basename(chrs_bim[chr])), "S",subsets, sep="")
pathout = paste("folderOut/Data/Subsets/",outfile, sep="")
write.table(dataout, pathout, col.names=FALSE, row.names=F)
}
rm(snp_data); rm(LDsubset)
stop = Sys.time()
print(stop-start)
}
答案 0 :(得分:0)
该行:
pathout = paste(folderOut/Data/Subsets/",outfile, sep="")
缺少开头双引号。它应该是:
pathout = paste("folderOut/Data/Subsets/", outfile, sep="")
我不确定这是否完全解决了您的问题,但这应该会有所帮助。