Independent samples update

[runjin326]

Purpose/implementation Section

Change "secondary" to "relapse" to only capture tumor_descriptor == c("Recurrence", "Recurrent Tumor","Recurrent tumor","Progressive","Progressive Disease Post-Mortem") Additional rnaseq independent sample lists are generated

What was your approach?

Added relapse_descs <- c("Recurrence", "Recurrent Tumor","Recurrent tumor","Progressive","Progressive Disease Post-Mortem") and use this as a filter

What GitHub issue does your pull request address?

https://github.com/PediatricOpenTargets/ticket-tracker/issues/75

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

Please double check all the modifications

Which areas should receive a particularly close look?

Please check the logics in calling rnaseq independent samples - currently: independent-specimens.rnaseq.primary.tsv is matched primary + RNA only primary independent-specimens.rnaseq.relapse.tsv is matched relapse + RNA only relapse

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

Yes

Results

See /results folder.

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

.tsv files

What is your summary of the results?

wc -l *.tsv 11580 independent-specimens.rnaseq.primary-plus.tsv 11043 independent-specimens.rnaseq.primary.tsv 252 independent-specimens.rnaseq.relapse.tsv 1127 independent-specimens.wgs.primary-plus.tsv 999 independent-specimens.wgs.primary.tsv 168 independent-specimens.wgs.relapse.tsv 168 independent-specimens.wgs.secondary.tsv 1865 independent-specimens.wgswxspanel.primary-plus.tsv 1735 independent-specimens.wgswxspanel.primary.tsv 173 independent-specimens.wgswxspanel.relapse.tsv 173 independent-specimens.wgswxspanel.secondary.tsv 29283 total

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.