Step 2 of DGE analysis of matched polya and stranded samples

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This is the second one of the four pull requests for creating the PediatricOpenTargets/OpenPBTA-analysis/analysis/rna-seq-protocol-dge analysis module. These four pull requests correspond to the following four analysis steps:

1. Collapse pbta-gene-counts-rsem-expected_count matrices of stranded and poly-A libraries using the OpenPBTA-analysis/analyses/collapse-rnaseq analysis module.
2. Generate a HTML report of the collapsed genes using the OpenPBTA-analysis/analyses/collapse-rnaseq analysis module.
3. Run edgeR exactTest, glmLRT, and glmQLFTest comparing stranded and poly-A RNA-seq rsem-expected_counts, using an adapted workflow from the OMPARE project.
4. Select genes that are stably expressed in poly-A and stranded RNA-seq libraries.

The overall purposes of the PediatricOpenTargets/OpenPBTA-analysis/analysis/rna-seq-protocol-dge module are:

• Check if the DGE analysis between polya and stranded data follow a null-p-value distribution.
• Determine stably expressed transcripts between polyA and stranded samples.

Purpose/implementation Section

What scientific question is your analysis addressing?

Generate a HTML report of the collapsed genes using the OpenPBTA-analysis/analyses/collapse-rnaseq analysis module.

What was your approach?

Use the OpenPBTA-analysis/analyses/collapse-rnaseq/02-analyze-drops.Rmd by changing the input and out filenames in run-rna-seq-protocol-dge.sh line 34-47 (pasted below).

# run the notebook for analysis of dropped genes
Rscript -e "rmarkdown::render(input = '02-analyze-drops.Rmd', params = list(polya.annot.table = 'results/pbta-gene-counts-rsem-expected_count-collapsed_table.polya.rds', stranded.annot.table = 'results/pbta-gene-counts-rsem-expected_count-collapsed_table.stranded.rds'), clean = TRUE)"

mv '02-analyze-drops.nb.html' 'results/expected_count-collapse-gene-drops.nb.html'

What GitHub issue does your pull request address?

d3b-center/ticket-tracker-OPC#17

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Can 02-analyze-drops.Rmd, which is copied from the OpenPBTA-analysis/analyses/collapse-rnaseq module, be directly applied to results/pbta-gene-counts-rsem-expected_count-collapsed_table.polya.rds and results/pbta-gene-counts-rsem-expected_count-collapsed_table.stranded.rds as in the line 35 of run-rna-seq-protocol-dge.sh (pasted below)?

Rscript -e "rmarkdown::render(input = '02-analyze-drops.Rmd', params = list(polya.annot.table = 'results/pbta-gene-counts-rsem-expected_count-collapsed_table.polya.rds', stranded.annot.table = 'results/pbta-gene-counts-rsem-expected_count-collapsed_table.stranded.rds'), clean = TRUE)"

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)?

• results/expected_count-collapse-gene-drops.nb.html: HTML report of the collapsed genes in results/pbta-gene-counts-rsem-expected_count-collapsed_table.polya.rds and results/pbta-gene-counts-rsem-expected_count-collapsed_table.stranded.rds, generated by 02-analyze-drops.Rmd.

Documentation Checklist

• This analysis module has a README and it is up to date.
• The analytical code is documented and contains comments.

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Closed as discussed in #8.