top 3 from pathways="auto" different from top common pathways from OncogenicPathways()

[AnitaS321]

Hello,
I would like include on my oncoplot the top 3 pathways I see when using OncogenicPathways function. I cannot figure out why the reported Fraction_mutated_samples is different depending on the function used as the maf is the same. Or, is it choosing from the top 3 based on the genes shown in the oncoplot? Is there a way to simply choose the names of the pathways I want to include from OncogenicPathways() function, without having to create a tsv file that lists each gene for my chosen pathways? I have removeNonMutated = FALSE so that all samples should be considered. Thanks in advance for any help!

[PoisonAlien]

Hi,

Sorry for the tardy response. Just got back to work.
Just to confirm, oncoplot and OncogenicPathways both use different sources for pathways.

1. oncoplot uses pathways from derived from driver genes. Source
2. OncogenicPathways uses pathways from the TCGA publication

Hope this helps.

[AnitaS321]

No worries - thank you so much for explaining!