txt to .maf format

Question

[Maryam]

Hello,

I am trying to import my variant file with all the required maf columns in R studio

Chr Start   End Ref Alt Gene.refGene    GeneDetail.refGene  ExonicFunc.refGene  AAChange.refGene    Tumor_Sample_Barcode    Func.refGene

using this code;

var.annovar2 <- system.file("extdata", "mutation.hg19_multianno.txt", package = "maftools")

But imported file is empty

Kindly can someone help me please what am missing

Thank you

[4galaxy77]

.txt isn't a format. Please edit your question to show a sample of the .txt file.

Answer 1

[Ram]

Really late answer but here it goes anyway.

I looked at maftools' github history for inst/extdata for the past 6 years, and I don't see the file mutation.hg19_multianno.txt. From the naming conventions being used by PoisonAlien, this doesn't feel like a file that they would include, which means it's probably a custom file you're supplying.

I'm also assuming that there's some sort of error message you're not observing or not reporting here, because you should see a file not found error as you're trying to read a non-existent file. Use read.maf with the absolute path to the file you're trying to read in, as system.file is used to load files supplied by the package, not your own files.