ssm_to_proteinpaint function needed

[rdmorin]

We need a function that takes a data frame in MAF format and generates an input file for ProteinPaint using the mutations in the MAF.

It should optionally add one or more of the optional columns that ProteinPaint can accept (using information in the GAMBL metadata).

[rdmorin]

@vladimirsouza has this been completed?

[vladimirsouza]

Yes. This has been addressed in this open PR and is waiting for approval.

[rdmorin]

Can @mattssca or @Kdreval or @HoumanLM review this please?

[Kdreval]

Yes that PR is under review and there few outstanding things to address/improve. It was updated to resolve those and I will review it today 👍

[HoumanLM]

I have two small suggestions:
For the checking the columns and printing error message in case some of them are not in the file, maybe it would be better if we summarize the code to make it easier to understand. For example, we can change it to this code:

• if (any(!(maf_req_cols %in% names(maf_data)))) {

• missing_cols <- maf_req_cols[!(maf_req_cols %in% names(maf_data))]
  

• stop(paste("Required columns missing in the input MAF data frame:", paste(missing_cols, collapse = ", ")))
  

• }

The other thing is about coding_only param which might be better if we make its default value to "TRUE" as we are going to consider variants in the context of proteins.

[mattssca]

Thanks, Houman! The PR is merged. Please post your suggestions for enhancement under the correct repo (GAMBLR.viz) for this function as a new issue and mark it with the enhancement tag (or any other tag you seem fit).

[HoumanLM]

Sure Adam! Thanks!