Updated analysis: methylation summary module

[ewafula]

What analysis module should be updated and why?

Update methylation-summary modules

What changes need to be made? Please provide enough detail for another participant to make the update.

• update the module to utilize RNA-Seq and methyl independent sample lists
• update module to compute gene locus-isoforms in addition to gene locus for beta-tpm correlations
• create separate gene-level and isoform-level methylation summary tables to reduce the file size

What input data should be used?

• infinium-methylationepic-v-1-0-b5-manifest-file-csv.zip
• gencode.v39.primary_assembly.annotation.gtf.gz
• independent-specimens.rnaseqpanel.primary-plus.eachcohort.tsv
• independent-specimens.methyl.primary-plus.eachcohort.tsv
• gene-expression-rsem-tpm-collapsed.rds
• rna-isoform-expression-rsem-tpm.rds
• ensg-hugo-pmtl-mapping.tsv.tsv
• methyl-beta-values.rds
• efo-mondo-map.tsv
• histologies.tsv

When do you expect the revised analysis will be completed?

Before the v12 data release

Who will complete the updated analysis?

@ewafula

[chinwallaa]

is there a concern on the size of the raw and summary tables - only being used by the API and possibly by FNL for backend for MTP use. May be too large to run on a local laptop, currently on Isilon and EC2? isoform table can be seperate table. (to enable gene w/ isoform plots). This needs to be ported/migrated to a CAVATICA app when ready.