How to merge multiple MAF files into one MAF file ?

[GAUSS66-well]

Hello, I'm a rookie of R language. I want to merge multiple MAF files into one MAF file and export table or txt file to my computer. All MAFS are in one folder. What should I do? thanks a lot.

[PoisonAlien]

Hi,
Sorry for the late reply. You could just list all the maf files and use the function marge_mafss().

maf_files = list.files(path = "D:\downs\mutation\files", pattern = "*.\\.maf\$", full.names = TRUE)
mymaf = maftools::merge_mafs(mafs = maf_files, verbose = TRUE)
maftools::write.mafSummary(maf = mymaf, basename = "mymaf")

Hope this helps.

[GAUSS66-well]

wow,it has worked !! thank you so much!

[amarinderthind]

This function does not seem to retain sample info but merges all file variants in one sample name after removing duplicate variants.

[amarinderthind]

@PoisonAlien Got it supposed to rename, Source_MAF to Tumor_Sample_Barcode. But the issue is it removes variants, in the first place, by considering them duplicates (Even though they belong to different samples).