将 MAF 文件转换为数据表时 data.table::fread 错误

Question

我想将 50 个 MAF 文件与示例信息合并，以便我可以将其作为 data.table 读取并对其进行子集化。

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/发布/bioc/manuals/maftools/man/maftools.pdf

Answer 1

当我运行你的代码时，maf确实没有指向任何字符（“”），这当然不能被fread读取。但是，当我尝试时，

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

它会按预期工作。