What scientific question is your analysis addressing?
Run chromosomal instability
What was your approach?
This module also needed to be divided into script to run for subtyping and plot scripts to not run. I added that code to the bash script.
01-localization-of-breakpoints.Rmd was not set up to intake either histologies file, so I added that. However, when I tried to run the OPENPBTA_BASE_SUBTYPING=1 bash ../analyses/chromosomal-instability/run_breakpoint_analysis.sh, I get an error:
Quitting from lines 150-154 (01-localization-of-breakpoints.Rmd)
Error: '../../data/pbta-histologies.tsv' does not exist in current working directory ('/home/rstudio/kitematic/analyses/chromosomal-instability').
So I am not sure where the logic is going wrong.
In the meantime, I changed the param to 1 inside of the Rmd and ran it, to get the analysis file, in order to continue the PRs.
What GitHub issue does your pull request address?
1426 partial
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
logic for choosing histology file
Is there anything that you want to discuss further?
Also note, this 01 script requires short_histology
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?
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.
Purpose/implementation Section
What scientific question is your analysis addressing?
Run chromosomal instability
What was your approach?
This module also needed to be divided into script to run for subtyping and plot scripts to not run. I added that code to the bash script.
01-localization-of-breakpoints.Rmdwas not set up to intake either histologies file, so I added that. However, when I tried to run theOPENPBTA_BASE_SUBTYPING=1 bash ../analyses/chromosomal-instability/run_breakpoint_analysis.sh, I get an error:So I am not sure where the logic is going wrong.
In the meantime, I changed the param to 1 inside of the Rmd and ran it, to get the analysis file, in order to continue the PRs.
What GitHub issue does your pull request address?
1426 partial
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
logic for choosing histology file
Is there anything that you want to discuss further?
Also note, this 01 script requires short_histology
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?
Reproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.