Mutations across studies

[Akshaya Vs]

I want to gather mutation information (such as variant info, depth, maf) across all the targeted sequencing. I tried cbioportR in rstudio using get_mutations_by_study function and the column are not same. How do I circumvent this problem? would cBioPortalData package help?

Thank you for your help.

PhD student

[Benjamin Gross]

Hi,

According to documentation, get_mutations_by_study should return a data frame in MAF file format, so the returned format should be standard.  If I understand your question, it may be that not all information (columns) are available across all studies you are querying.   If this is true, using cBioPortalData package will not help.  Have you checked what data is available in the cbioportal.org website or flat files (MAFs) first?

Also, it may be useful to reach out to maintainer of the cbioportalR and provide example to confirm:

Let us know if you have any further questions.

-Benjamin

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