r-data.table::将MAF文件转换为数据表时发生fread错误

Question

我想将50个MAF文件与样本信息合并，这样我就可以将其作为数据表读取并对其进行子集设置。

library(maftools)
# Load MAF files
maf = system.file("extdata", list.files(path="mafs/"), package="maftools")
# Load sample information
si <- system.file("extdata", "sample-information.tsv", package="maftools")
d = read.maf(maf=maf, clinicalData=si)

追溯：

Error in data.table::fread(file = maf, sep = "t", stringsAsFactors = FALSE,  : 
File '' does not exist or is non-readable. getwd()=='C:/Users/User/Documents/VanAllen'
> traceback()
3: stop("File '", file, "' does not exist or is non-readable. getwd()=='", 
getwd(), "'")
2: data.table::fread(file = maf, sep = "t", stringsAsFactors = FALSE, 
verbose = FALSE, data.table = TRUE, showProgress = TRUE, 
header = TRUE, fill = TRUE, skip = "Hugo_Symbol", quote = "")
1: read.maf(maf = maf, clinicalData = si)
1: data.table::fread(input = maf)

Maftools文档：https://www.bioconductor.org/packages/release/bioc/manuals/maftools/man/maftools.pdf

Answer 1

当我运行您的代码时，maf确实没有指向任何字符("(，这当然是fread无法读取的。然而，当我尝试时

fread("R/x86_64-pc-linux-gnu-library/3.6/maftools/extdata/brca.maf.gz")

它按预期工作。