#932 Part N Kinase domain overlap as hotspot

[kgaonkar6]

⚠️ merge #932 before this PR

Purpose/implementation Section

What scientific question is your analysis addressing?

We would like to gather all unique sites overlapping the kinase domain as snv/indel hotpsots in our dataset which are not Cosmic Census genes or in MSKCC cancer hotspots.

What was your approach?

I used biomaRt and files downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/pfamDesc.txt.gz and http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ucscGenePfam.txt.gz .

After gathering kinase domain locations I gathered mutation sites that overlap kinase domain as hotspots.

What GitHub issue does your pull request address?

#932

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Does the function gathering the pfam location seem OK? I'm not sure how to version the downloaded pfam files might get out of date, not sure?

Is there anything that you want to discuss further?

I only used PF00069 domain, do we want to look at other kinase domains?

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Yes

Results

What types of results are included (e.g., table, figure)?

tables

What is your summary of the results?

2178 unique sites per Kids_First_Biospecimen_ID overlap a PF00069 domain location

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.