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Subset files for ATRT scripts #325
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- Add `00-subset-files-for-ATRT.R` - Adapt `01-ATRT-molecular-subtyping data-prep.Rmd` to use subset files
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| dplyr::summarise( | ||
| HALLMARK_MYC_TARGETS_V1 = mean(HALLMARK_MYC_TARGETS_V1), | ||
| HALLMARK_MYC_TARGETS_V2 = mean(HALLMARK_MYC_TARGETS_V2), | ||
| HALLMARK_NOTCH_SIGNALING = mean(HALLMARK_NOTCH_SIGNALING) | ||
| ) |
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You appear to be repeating this step in the next notebook.
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| #### Filter ssGSEA data -------------------------------------------------------- | ||
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| # Calculate ssGSEA mean and sd |
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Before you calculated the z-score, I would subset this to ATRT samples. Which I don't think you've done unless I missed it.
…into subset-ATRT-files
- Subset ssGSEA files before calculating the zscore - rerun nb
…into subset-ATRT-files
…BTA-analysis into subset-ATRT-files
- FIx ssgsea naming in code - rerun nb
jaclyn-taroni
approved these changes
Dec 12, 2019
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This looks good! Two things I'd like to see before it gets merged:
- The TODO for the GISTIC stuff (Proposed Analysis: Molecularly subtype ATRT tumors #244 (comment))
- Add the start of the README here (not the usage, etc.) with a note that warns folks about what release of the data that you used to generate the subset files, e.g., if you run this again you might want to make sure the ATRT subset files are regenerated with the most recent release.
| data.table::fread(file.path(root_dir, | ||
| "data", | ||
| "pbta-snv-consensus-mutation-tmb.tsv")) | ||
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Let's add a TODO re: SV data / GISTIC output here please.
- Add TODO comment in `00-subset-files-for-ATRT` indicating plan to incorporate SV data/GISTIC output
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00-subset-files-for-ATRT.R01-ATRT-molecular-subtyping data-prep.Rmdto use subset filesPurpose/implementation Section
The purpose of this PR is to subset the files for the ATRT molecular subtyping scripts.
What scientific question is your analysis addressing?
This analysis addresses the molecular subtyping of ATRT samples question.
What was your approach?
I subset the histologies, focal copy number, ssGSEA pathways, tumor mutation burden, and RNA expression files for ATRT samples using the
sample_idvariable in the histologies file to match samples.What GitHub issue does your pull request address?
This PR addresses issue #244.
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
Yes, this analysis is ready for review.
Results
What types of results are included (e.g., table, figure)?
The output files of this PR include the subset files as follow:
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atrt-subset/atrt_focal_cn.tsv.gz-
atrt-subset/atrt_histologies.tsv-
atrt-subset/atrt_ssgsea.tsv-
atrt-subset/atrt_tmb.tsv-
atrt-subset/atrt_zscored_expression.RDSWhat is your summary of the results?
Reproducibility Checklist