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thelovelab / tximport

Transcript quantification import for modular pipelines
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Unexpected behavior when processing RSEM transcript level files #15

Closed ecoenen closed 8 years ago

ecoenen commented 8 years ago

I used this line of code to process RSEM ".isoforms.results" files: txi.RSEM <- tximport(files, type = "rsem", reader = read_tsv, txIn = TRUE, txOut = TRUE) The rownames of the resulting list objects, are gene ID's, which is not what I expected, since I put the txOut option to true.

When I explicitly define the column names like in the line of code below, it works like expected (the rownames of the resulting list objects are now transcript ID's): txi.RSEM <- tximport(files, type = "none", geneIdCol = "gene_id", txIdCol = "transcript_id", abundanceCol = "TPM", countsCol = "expected_count", lengthCol = "length", reader =
read_tsv, txIn = TRUE, importer = read.delim, txOut = TRUE)

mikelove commented 8 years ago

Yup. I haven't had time to work on this, but I had already filed it as an issue to remind myself:

https://github.com/mikelove/tximport/issues/11

Bioconductor is in feature freeze right now in preparation for a new release. But this is on my short list of issue to address next cycle.