Anand Mayakonda

Hi, Thanks for sharing. I will see what I can do. Btw, you'd like to use these results to merge with MAF and further visualizations rite? for example, oncoplot with...

Hello, You could try `sepwd_genes`, `sepwd_samples` arguments. These options are only available in GitHub version. Let me know if this helps.

Ah, I see what you mean. Unfortunately its not possible for now. But, I can push some changes for this. I will update you when its done.

Hi, Is it possible to share a plot to demonstrate? I am guessing you would like to have VAF on the y-axis instead of frequency?

Hi, Could you please make sure that the annovar output has all the required columns that are highlighted in the error message?

Hi, It returns the converted data in MAF format. You can run the function with `MAFobj = TRUE` and, it should be enough for you to pass it to most...

Hi, Please check `?annovarToMaf` for all available options. If you want to generate an maf file, check out the argument `basename`.

Hi, CNV is not used for TMB estimation. Could you please double-check again? ```r CNV_maftools

Hi @MjelleLab , Sorry for the late response. I am guessing of two possibilities, 1. Can you check if the individual MAF files (from vcf2maf) have the column name `Tumor_Sample_Barcode`?...

This is already taken care of in #207. Since the clnicalfeature is not a numeric - its plotted as a categorical variable. You coudl try the below and it should...