How to get vafCol converting annovar outputs to maf object

Question

[MS]

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

Answer 1

[Getting there]

You need to tell inferHetrogeneity what the vaf column is called, using vafCol = 'column name' if it is not a default name. Ie

inferHeterogeneity(laml, vafCol = 'column name')