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