supp tables modified

[runjin326]

Purpose/implementation Section

What scientific question is your analysis addressing?

Modify supplementary tables to do the following: 1) Remove alexandrov and cosmic mutational signatures from DNA table 2) Add new tab for quantiseq immune scores to RNA-Seq file (probably easiest to do column 1 bs_id and 10 colunns for cell types)

What was your approach?

1) Removed alexandrov and cosmic mutational signatures sheets 2) Used fitted_exposures_signal-cns_sigfit.rds not fitted_cns_signature_exposures.RDS for the output (there was a changed in the input) 3) Add quantiseq_immune as the 3rd sheet for RNA results.

What GitHub issue does your pull request address?

https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/1260

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

Which areas should receive a particularly close look?

Please check to see whether the name quantiseq_immune is what you want.

Is there anything that you want to discuss further?

No

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)?

Excel sheets with outputs.

What is your summary of the results?

NA

Reproducibility Checklist

• [x] 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

• [x] 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.
• [x] The analytical code is documented and contains comments.

[runjin326]

@jharenza - sorry about that - done.