add kinase domain retention info to putative oncogenic file

d3b-center / annoFuse

Filter and prioritize fusion calls

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add kinase domain retention info to putative oncogenic file #66

Closed jharenza closed 4 years ago

jharenza commented 4 years ago

add kinaseGeneDomainRetained and rename GeneLoc -> kinaseDomainGeneLoc

kgaonkar6 commented 4 years ago

Since I'm adding the this as part of the annotate_fusion_calls() , should we keep them as generic columns DomainRetained , GeneLoc and then I can change the name to kinaseGeneDomainRetained and kinaseDomainGeneLoc specifically for demo file?

Or we only want to check for kinase domain so keep them hardcoded as kinaseGeneDomainRetained and kinaseDomainGeneLoc column names?

federicomarini commented 4 years ago

As long as

these are not hard coded in the functions of annoFuse
they do not belong to the default columns to be found

... I have no problem with either approach

kgaonkar6 commented 4 years ago

I actually think adding kinaseGeneDomainRetained and kinaseDomainGeneLoc was adding more rows to the fusion calls with status for each Gene1A and Gene1B creating a new row per Fusion (Gene1A--Gene1B).

So I've added "DomainRetainedInGene1A" ,"DomainRetainedInGene1B" which doesn't add rows .The domain retention code to fusion_driver() function since it seems to be more of a project specific criteria, does that sound ok?

jharenza commented 4 years ago

close with #70