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thelovelab / tximport

Transcript quantification import for modular pipelines
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Returns TPM when abundanceCol is set to any value for type='rsem' #44

Closed csmith-pact closed 3 years ago

csmith-pact commented 4 years ago

Desired behavior is to return FPKMs when abundanceCol='FPKM' and throw an error if an invalid value is set - TPMs are returned regardless of its value currently without a warning to the user.

e.g. tximport(files, type = "rsem", txIn = FALSE, txOut = FALSE, abundanceCol = 'FPKM')

tximport_1.18.0

mikelove commented 4 years ago

I think this one will resolve:

https://support.bioconductor.org/p/134119/#134121