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thelovelab / tximport

Transcript quantification import for modular pipelines
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feature request: modularize gene-level summarization when txOut=TRUE #12

Closed stephenturner closed 8 years ago

stephenturner commented 8 years ago

I wanted to use tximport to read in a bunch of sailfish output files then write out abundances/counts for both genes and transcripts. I ended up doing the import twice, once for txOut=TRUE and once where it was FALSE. Would be nice to allow usage where txOut=FALSE, then apply a later function that would perform the summarization as a separate step.

e.g.

txdata <- tximport(files, txOut=FALSE)
gndata <- txGeneSum(txdata)
mikelove commented 8 years ago

makes sense. I'll think on restructuring the code.

mikelove commented 8 years ago

hi Stephen,

good suggestion. helped me to shorten average function length while i'm at it.

when you have time, try out version 0.0.19 with summarizeToGene. example in the beginning of the vignette.