Dear all,

please could you advise on the following: I am using MAFTOOLS in order to convert an ANNOVAR file into a MAF file, for downstream analyses; however, I am getting the error message below --- any insights please about how to fix it ? thank you very much ;) !

ann.file<-read.delim("vcf.test.annovar",header=T)

ann.file$Tumor_Sample_Barcode <- "Sample_Test"
write.table(ann.file, file="ann_test.txt", row.names = FALSE, sep = "\t", quote = FALSE)

var.annovar.maf = annovarToMaf(annovar = "ann_test.txt",
                               Center = 'STANFORD', refBuild = 'hg38',
                               tsbCol = "Tumor_Sample_Barcode",table = 'refGene')

the code above works. However, when doing "getSampleSummary(var.annovar.maf)" it says :

Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘getSampleSummary’ for signature ‘"data.table"’

Hi,

You need to return it as an MAF object. 

var.annovar.maf = annovarToMaf(annovar = "ann_test.txt",
                               Center = 'STANFORD', refBuild = 'hg38',
                               tsbCol = "Tumor_Sample_Barcode",table = 'refGene', MAFobj = TRUE)

Hi Anand, please may I ask you, why do the following 2 pieces of R code give different results :

-- piece 1 :

var.annovar.maf = annovarToMaf(annovar = "vcf.test.annovar_MANY.txt",
                               Center = 'STANFORD', refBuild = 'hg38',
                               tsbCol = "Tumor_Sample_Barcode",table = 'refGene', MAFobj = TRUE)

MAF <- var.annovar.maf

getSampleSummary(MAF)
getGeneSummary(MAF)
getFields(MAF)

plotmafSummary(maf = MAF, rmOutlier = TRUE, addStat = 'median', dashboard = TRUE)

-- piece 2 :

var.annovar.maf = annovarToMaf(annovar = "vcf.test.annovar_MANY.txt",
                               Center = 'STANFORD', refBuild = 'hg38',
                               tsbCol = "Tumor_Sample_Barcode",table = 'refGene')

MAF = read.maf(maf = var.annovar.maf, removeSilent = TRUE, useAll = FALSE)

getSampleSummary(MAF)
getGeneSummary(MAF)
getFields(MAF)

plotmafSummary(maf = MAF, rmOutlier = TRUE, addStat = 'median', dashboard = TRUE)