Tximport "sclaedTPMs" imports NumReads column from Salmon output

Question

[anna]

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?

Answer 1

[jared.andrews07]

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.