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Update RNA expression of copy number losses #493
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- implement command line options in `rna-expression-validation.R` and `run-prepare-cn.sh` scripts - adjust custom functions scripts to reflect command line options
- perform log transforming and zscoring on matrix first in `calculate_z_score` function - propagate changes in `merge_expression` function and in `rna-expression-validation.R` script
- run script using polyA expression data for each of the files in `results` (stranded was not run as it was not able to successfully be completed on my local machine due to memory) - introduce a for loop in the shell script that will run through each of the files in `results` for polyA and stranded expression data (this is commented out until the consensus file has a subset that can be used in circleci) - old plots are replaced with the new plots reflecting the zscore polyA data
- uncomment for loop in shell script - add stranded plots for cnvkit, controlfreec, and consensus annotated files (autosomes and x/y files)
cbethell
changed the title
- add space in square bracket to fix syntax warning
- fix object name in rna-expresssion-functions.R script - run rna-expression-validation.R script on cnvkit autosome annotated data with polya expression
- updated `display-plots.md` to display only the consensus seg file plots
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- update `README` files to reflect changes to the focal -cn-file-preparation module in PR AlexsLemonade#493
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jaclyn-taroni
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Feb 7, 2020
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👍 I think this is correct and headed in the direction we want to go (e.g., skipping original caller files by default). As you noted on #387, we are looking to add density plots. We would not necessarily expect all losses to show changes when we look at z-scores (it depends on the gene!) and I have some ideas about where we would go next that I want to marinate on and discuss next week.
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- update `README` files to reflect changes to the focal -cn-file-preparation module in PR #493 Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
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Purpose/implementation Section
The purpose of this PR is to update/revamp the analysis involving RNA expression of copy number losses.
Command line options are implemented, the expression files are updated to use the collapsed files found in the
datadirectory, and the custom functions are refactored.What scientific question is your analysis addressing?
Do the RNA expression scores of copy number loss calls agree that these calls should be losses?
What GitHub issue does your pull request address?
This PR addresses issue #387.
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
The
calculate_z_scoreandmerge_expressionfunctions found in therna-expression-functions.Rscript are edited in this PR in an attempt to speed up the analysis. These functions should be checked for correctness.Note: For the purpose of plotting, I am using the z-score values (as opposed to the log transformed values that were being used before this PR). I noticed that we were calculating the zscore values but not actively using them, if there are any objections to this I can revert this change.
Note 2: The plots using the stranded expression file in this PR were generated using the subsetted file in the
testingdirectory (the script does not successfully run on my local machine due to the magnitude of the stranded data).Is there anything that you want to discuss further?
plotsdirectory. That being said, should we only represent the plots that utilize the consensus seg annotated file? In doing so, we would also be improving the time it takes to run this module as it would not need to loop through the larger CNVkit and Controlfreec annotated files (my idea for this would be putting the annotated consensus files in their own directory and having the shell script loop over the files in there).Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
Yes, this PR is ready for review.
Results
What types of results are included (e.g., table, figure)?
The results include plots for CNVkit, Controlfreec, and the consensus annotated files for each expression file (polyA and stranded).
What is your summary of the results?
Reproducibility Checklist
No new dependencies are included in this PR.
Documentation Checklist
I will update the
READMEto include the plots generated with this module once we determine which plots we want to keep and/or remove.READMEand it is up to date.analyses/README.mdand the entry is up to date.