v12 rnaseq expression summary stats

[ewafula]

Purpose/implementation Section

What scientific question is your analysis addressing?

Update rna-seq-expression-summary-stats for v12

What was your approach?

• included TCGA RNA-Seq expression data
• no longer using R jsonlite::josn for JSON format conversion due to R limitations in memory allocation for large files
• errors out with much larger v12 expression data matrices - R character strings are limited to 2^31-1 bytes
• now using bash script with command line utilities for JSON conversion
• results tables to large and no longer uploaded on GitHub

What GitHub issue does your pull request address?

• update rna-seq-expression-summary-stats tables for v12  ticket-tracker-OPC#530

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

Which areas should receive a particularly close look?

• review code update to include TCGA RNA-Seq expression data
• review the code update for JSON format conversion

Is there anything that you want to discuss further?

NA

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)?

tables

What is your summary of the results?

Regenerate results the module results/ folder

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.

[sangeetashukla]

I have reviewed the merge for OPC and TCGA input files, and the change in the bash script for creating json files instead of doing that with the R script. I corroborated the failure of R to handle the larger files while creating json and agree that this change is justified.

[zzgeng]

The code works fine. It included RNA-seq from TCGA. Bash script generated json files. Approving!