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"’