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Update focal CN file prep to use exons again and cover the consensus SEG case #479
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Add ploidy!
Also rerun + use $XYFLAG for the consensus step
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Rendered version of the notebook here: https://jaclyn-taroni.github.io/openpbta-notebook-concept/02-add-ploidy-consensus.nb.html |
cansavvy
approved these changes
Jan 28, 2020
| # of the repository as follows: | ||
| # | ||
| # Rscript 'analyses/oncoprint-landscape/01-prepare-cn-file.R' | ||
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Unless this script would work without specifying anything, I suspect this usage example is incomplete?
| The mapping is limited to _coding sequences_. | ||
| Mapping to cytobands is performed with the [`UCSC hg38 cytoband file`](http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cytoBand.txt.gz). | ||
| _Note: The decision to implement the `UCSC file` was made based on a comparison done between the cytoband calls in the `org.Hs.eg.db` package and the calls in the `UCSC file`. We found that they disagreed in ~11,800 calls out of ~800,000 and the `UCSC file` contains more cytoband calls._ | ||
| * `02-add-ploidy-consensus.Rmd` - This is very similar to the CNVkit file prep. |
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I am unsure what this is referring to:similar to CNVKit file prep can you put a link to what this is referring to?
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I added the 01 notebook file name here to make it more clear.
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| * `02-rna-expression-validation.R` - This script examines RNA-seq expression levels (RSEM FPKM) of genes that are called as deletions. | ||
| * `rna-expression-validation.R` - This script examines RNA-seq expression levels (RSEM FPKM) of genes that are called as deletions. | ||
| It is not currently run via the shell script. |
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What's the plan for this script then? Is it being dropped or revamped or is it supposed to be called somewhere else?
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Plan is to rework it #387
Co-Authored-By: Candace Savonen <cansav09@gmail.com>
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Purpose/implementation Section
We used to use exons to annotate CNV data files the prior to #452, which made the switch to using coding regions. That looked like it was too restrictive and inconsistent with what is typically done (some references and quotes supplied by @cbethell below).
Monlong et al. NAR. 2018.:
Bailey et al. Cytogenet Genome Res. 2009.:
What was your approach?
Here we are:
analyses/focal-cn-file-preparation/02-add-ploidy-consensus.Rmd). There is a lot of overlap with how we prepare the CNVkit file, so this can probably be refactored in a subsequent pull request. This basically means this code was reviewed before in Update CNV segment to gene mapping: support both formats, use GTF, etc. #253 and Add X and Y chromosomes to CNV segment to gene symbol mapping #259.analyses/focal-cn-file-preparation/03-prepare-cn-file.Rfile prior to Update/Revampfocal-cn-file-preparationmodule #452, with some minor changes (making the option name for SEG files more general): https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/2af3f350a247d66f68fe9305224d937ee0e90a8c/analyses/focal-cn-file-preparation/01-prepare-cn-file.R (This script has been renumbered as part of this pull request.)masterat the moment. We're also skipping the expression step currently.What GitHub issue does your pull request address?
Closes #473; related to #186
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
This looks a bit worse than it is, as most of the code has gone through review before (sorry!)
Reproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.