How to get vafCol converting annovar outputs to maf object

How to get vafCol converting annovar outputs to maf object

0

Hi,

I am trying to find heterogeneity in tumor samples using maftools.

I have annovar outputs and converted them to maf object using annovarToMaf function.

var.annovar = system.file("extdata", "variants.hg19_multianno.txt", package = "maftools")
var.annovar.maf = annovarToMaf(annovar = var.annovar, Center="CSI-NUS", refBuild = 'hg19', 
                               tsbCol="Tumor_Sample_Barcode", table="ensGene")

Then I am reading maf file with readmaf:

laml.maf <- read.maf(maf = var.annovar.maf)

When I tried inferHeterogeneity function it could not find vafcol. I also used system file example for annovartomaf but it gives same error.

So there could be additional step after converting annovar files to maf object before inferHeterogeneity function?
Thanks.

maf.het <- inferHeterogeneity(maf = laml)

laml.maf

An object of class  MAF 
                  ID summary  Mean Median
1:        NCBI_Build      NA    NA     NA
2:            Center      NA    NA     NA
3:           Samples       7    NA     NA
4:            nGenes       2    NA     NA
5:   Frame_Shift_Del       1 0.143      0
6: Missense_Mutation       3 0.429      0
7:             total       4 0.571   1


inferHeterogeneity


maftools


annovarToMaf

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