how to add new column in each maf dataframe?

[complexgenome]

Hi there,

I'm interested to visualize VAF in my cohort.

I don't have VAF column in my MAF files. I read that I can calculate using ratio of counts of ref and alt allele.
https://www.biostars.org/p/161298/#161777

I've following code:

maf_files = list.files(path = "edited_mafs_no_duplicates/", pattern = "*.\\.maf", full.names = TRUE)

mafs_datatable = lapply(X = maf_files, function(x){
  data.table::fread(file = x, sep = "\t", select = required.fields, skip = "Hugo_Symbol")
})

mafs = data.table::rbindlist(l = mafs_datatable, use.names = TRUE, fill = TRUE, idcol = "Source_MAF")

mafs_read = maftools::read.maf(maf = mafs)

How do I add or calculate this column to the list of data frames I've?

[PoisonAlien]

Hi,

It depends on what columns your maf has. If your ref and alt counts are stored under t_ref_count and t_alt_count, you could add a new t_vaf as in below

mafs = data.table::rbindlist(l = mafs_datatable, use.names = TRUE, fill = TRUE, idcol = "Source_MAF")
mafs[,t_vaf := as.numeric(as.character(t_alt_count))/(as.numeric(as.character(t_ref_count)) + as.numeric(as.character(t_alt_count)))]

[complexgenome]

Hi @PoisonAlien
Thank you for looking into this.
I'd like to confirm for the VAF:

Can VAF not be, VAF=t_alt/((t_alt+t_ref)*2) since there are two copies.

Or VAF be VAF=t_alt/(t_ref) that is count of alt divided by ref only.

Your suggested way
VAF=t_alt/(t_alt+ t_ref)

Sorry this may see confusing.

[PoisonAlien]

Hi,
It's the option 3. You would like to estimate the frequency of the variant allele of the total depth.

[complexgenome]

Thanks.

[nogay]

Hi,

I thought it was related:

When we add a new column to a maf object, let's say I want to merge to columns:

maf@data@new_column <- paste(maf@data$Hugo_Symbol, maf@data$HGVSp_Short,sep = "_")

If I then use subsetMaf with the newly made column like so:

filtered_maf <- subsetMaf(maf, query = "new_column == 'CSF3R_p.D510H'")

I get a "Object 'new_column' not found amongst [Hugo_Symbol, ..." error. When I check the maf object I can't see this new column in maf@maf.silent. What is the correct way of adding new columns to our maf?

Thank you