Hi All,
I am having issues reading in MAFtools generated merged file from multiple patients. The readMaf gives error even-though I have more than 2 samples per patient. Second, thing I notice is it removes one of tumor sample and never gets stored. Is there any filtering on mutations while reading in maf files? I tried to debug but couldn't figure it out.
I think issue is happening post this line of code in readMaf function. Can you please help find solution for this?
maf <- Maf(data = data.table::setDT(data), sample.info = as.data.frame(sample.info),
nonSyn.vc = nonSyn.vc, ref.build = refBuild)
maf_patient_list[[patient]] <- maf
Hi All, I am having issues reading in MAFtools generated merged file from multiple patients. The readMaf gives error even-though I have more than 2 samples per patient. Second, thing I notice is it removes one of tumor sample and never gets stored. Is there any filtering on mutations while reading in maf files? I tried to debug but couldn't figure it out. I think issue is happening post this line of code in readMaf function. Can you please help find solution for this? maf <- Maf(data = data.table::setDT(data), sample.info = as.data.frame(sample.info), nonSyn.vc = nonSyn.vc, ref.build = refBuild) maf_patient_list[[patient]] <- maf