Hi,
My quant.sf output file from Salmon looks this way :
Name Length EffectiveLength TPM NumReads
trans939774eca46f7c64 372 180 0 0
trans51222ae146bd8f57 1500 196 0 0
transf096323beb05847e 253 79 0 0
transb698181cc84af00c 2550 196 0 0
I use next options to import a number of quant.sf files using tximport :
txi <- tximport(my_files_quant,type="salmon", txOut=TRUE, countsFromAbundance="scaledTPM")
I was expecting that with "scaledTPM" option I would import some type of TPMs (maybe like TPM*library size) However it looks like tximport simply imports NumReads column from quant.sf file.
What is "scaledTPM" function then?
•
written
by
anna •
1 answer
You're requesting transcript abundances rather than gene counts (txOut = TRUE), so that parameter is ignored, I believe.
As for what that parameter actually does, I highly recommend you read the function documentation.
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