The mutational-signatures module needs to be finalized, with the following overall goals. These goals replace previous 05 and 06 scripts/notebooks.
This PR:
Perform extraction of the 8 CNS Signal/RefSig signatures with two methods, deconstructSigs and sigfit. This is now performed in 05-fit_cns_signatures.R. This script saves two files contained the estimated signature exposures, one per methods:
Perform a brief comparison of the results from these two methods in 06-compare_cns_exposures.Rmd. Comparison shows overall high similarity.
Next PR:
Update this module with pub-ready visualizations which will live in an 07 notebook.
In the next PR, the overall analysis README.md and the specific mutational-signatures module README.md will be updated.
What GitHub issue does your pull request address?
1220
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Overall organization.
Is there anything that you want to discuss further?
There is a world in which 05just uses deconstructSigs and proceeds straight to 07, skipping any (then moot) comparisons which happen in the current 06. Plus, because the current approach does a quick evaluation of both methods, we don't actually end up saving time by visualizing the faster method. But, skipping the comparison seems less desirable for posterity and having fewer "magic" decisions in the pipeline.
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)?
New result files in results/, as well as some quick scatterplots in the 06 notebook. These are not meant for the publication.
What is your summary of the results?
sigfit and deconstructSigs give fairly consistent results, with the latter method being much faster. So, the latter method will be use for subsequent viz.
Reproducibility Checklist
[x] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
[x] 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.
[x] The analytical code is documented and contains comments.
Purpose/implementation Section
The
mutational-signaturesmodule needs to be finalized, with the following overall goals. These goals replace previous05and06scripts/notebooks.This PR:
deconstructSigsandsigfit. This is now performed in05-fit_cns_signatures.R. This script saves two files contained the estimated signature exposures, one per methods:results/fitted_exposures_signal-cns-deconstructSigs.RDSresults/fitted_exposures_signal-cns-sigfit.RDS06-compare_cns_exposures.Rmd. Comparison shows overall high similarity.Next PR:
07notebook.In the next PR, the overall analysis
README.mdand the specificmutational-signaturesmoduleREADME.mdwill be updated.What GitHub issue does your pull request address?
1220
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Overall organization.
Is there anything that you want to discuss further?
There is a world in which
05just usesdeconstructSigsand proceeds straight to07, skipping any (then moot) comparisons which happen in the current06. Plus, because the current approach does a quick evaluation of both methods, we don't actually end up saving time by visualizing the faster method. But, skipping the comparison seems less desirable for posterity and having fewer "magic" decisions in the pipeline.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)?
New result files in
results/, as well as some quick scatterplots in the06notebook. These are not meant for the publication.What is your summary of the results?
sigfitanddeconstructSigsgive fairly consistent results, with the latter method being much faster. So, the latter method will be use for subsequent viz.Reproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.