I'd like to read in transcript-level results from RSEM using the
tximport package, but this does not appear to be supported.
tximport vignette only describes importing
sample.genes.results (gene-level) data, and the
tximport::tximport function is hard-coded to set
txIn = FALSE when
type = "rsem" (see here). Also, in the same block of code, abundance results are read from the
FPKM column of the RSEM output and not the
TPM column. This appears to be inconsistent with the TPMs read in for Salmon and Kallisto.
Any thoughts on why these decisions were made? Changes to 1 allow transcript-level RSEM result, and 2 use TPMs instead of FPKMs, seem fairly quick.