以下是我的代码。我正在尝试获取以.idat
结尾的所有文件(~20000)的列表,并使用函数illuminaio::readIDAT
读取每个文件。
library(illuminaio)
library(parallel)
library(data.table)
# number of cores to use
ncores = 8
# this gets all the files with .idat extension ~20000 files
files <- list.files(path = './',
pattern = "*.idat",
full.names = TRUE)
# function to read the idat file and create a data.table of filename, and two more columns
# write out as csv using fwrite
get.chiptype <- function(x)
{
idat <- readIDAT(x)
res <- data.table(filename = x, nSNPs = nrow(idat$Quants), Chip = idat$ChipType)
fwrite(res, file.path = 'output.csv', append = TRUE)
}
# using mclapply call the function get.chiptype on all 20000 files.
# use 8 cores at a time
mclapply(files, FUN = function(x) get.chiptype(x), mc.cores = ncores)
在阅读和写入有关1200个文件的信息后,我收到以下消息:
Warning message:
In mclapply(files, FUN = function(x) get.chiptype(x), mc.cores = ncores) :
all scheduled cores encountered errors in user code
我该如何解决?