Inconsistent merging in RNA-seq RDS files

[komalsrathi]

File(s)

What data file(s) does this issue pertain to?

pbta-gene-expression-rsem-fpkm.polya.rds
pbta-gene-expression-rsem-fpkm.stranded.rds

Release

What release are you using?

release-v5-20190924

Link to OpenPBTA-manuscript

Put a link to the relevant section of the OpenPBTA manuscript here.

Question/issue

Looks like an issue when merging the RSEM files. In Gencode v27, the actual gene id-symbol mappings are:

ENSG00000168824.14 HGNC:18790 
ENSG00000170091.10 HGNC:24955

Example of inconsistent merging:

stranded:

input.dat <- '~/Projects/OpenPBTA-analysis/data/pbta-gene-expression-rsem-fpkm.stranded.rds'
expr <- readRDS(input.dat)
head(expr[grep("HGNC", expr$gene_id),1:5])
                            gene_id BS_QWNBZ9RJ BS_FEPRNEXX BS_P39SQPTS BS_M8WP5T16
12451       ENSG00000168824.14_HGNC       86.73       20.43       79.11        2.28
12750       ENSG00000170091.10_HGNC      105.13       36.66       71.74        8.33
58348 ENSG00000168824.14_HGNC:18790          NA          NA          NA          NA
58349 ENSG00000170091.10_HGNC:24955          NA          NA          NA          NA

and for polya:

input.dat <- '~/Projects/OpenPBTA-analysis/data/pbta-gene-expression-rsem-fpkm.polya.rds'
expr <- readRDS(input.dat)
head(expr[grep("HGNC", expr$gene_id),1:5])
                            gene_id BS_R7NTZR4C BS_C83TK159 BS_PXCPK5XS BS_JB43XBCQ
12451       ENSG00000168824.14_HGNC          NA          NA       17.08          NA
12750       ENSG00000170091.10_HGNC          NA          NA       27.80          NA
58348 ENSG00000168824.14_HGNC:18790        1.80       56.39          NA       10.26
58349 ENSG00000170091.10_HGNC:24955       41.26       61.57          NA       25.85

[komalsrathi]

@jharenza I don't think I have access to assign this to you.

[jaclyn-taroni]

I can help with that!

[jharenza]

Thanks, just added as an issue to our github, too!

[jharenza]

addressed in #223