make clean oncoprint branch, adding SF oncoprint (2/2)

[jharenza]

Purpose/implementation Section

❗ STACKED ON #380 - need to download new CNV file

What scientific question is your analysis addressing?

This PR replaces #375 because I messed it up with some large files in testing

I will need to add a new CNV file to the release. I have updated to use freec wxs in the consensus in OPC due to the XY artifacts.

What was your approach?

Here, we assess mutations in SF and spliceosome complex genes

What GitHub issue does your pull request address?

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

Which areas should receive a particularly close look?

Is there anything that you want to discuss further?

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

Results

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

What is your summary of the results?

[1] "128 tumors altered in 195 patients" (including CNVs, fusions, mutations) [1] "65.64 %"

[1] "102 tumors mutated in 195 patients" print(paste(round(length(unique(collapse_snv_dat_mut$match_id))/length(unique(matched_dna_samples$match_id))*100, 2),"%")) [1] "52.31 %"

Reproducibility Checklist

• [ ] The dependencies required to run the code in this pull request have been added to the project Dockerfile.

Documentation Checklist

• [ ] This analysis module has a README and it is up to date.
• [ ] The analytical code is documented and contains comments.

[jharenza]

@naqvia can you add the SF gene list and onco_matrix_SFs.tsv to a supplemental table (2?) and we can then comment on the number of alterations and mutations in SFs+spliceosome complex. Not many recurrent, but generally widespread actually!

[jharenza]

Closes #374

[jharenza]

Runs as expected. I think we can add the SF oncoprint to the splicing factor set of Figs (either main or suppl).

It's in supp figure 2b right now, and cited in text