Hello! I was using the following command to import salmon quantification with bootstraps
txi <- tximport(files, type="salmon", txOut=TRUE, dropInfReps=FALSE, varReduce=FALSE)
problem is the output lost the transcript names, just 1,2,3...for row names. It was fine when I use the following command, without bootstraps
txi <- tximport(files, type="salmon", txOut=TRUE, dropInfReps=TRUE)
Has anyone had similar issue?
I can't replicate this yet on my end. Maybe you can try this on your end and see if you can find a reproducible example. Perhaps it is a version issue (always note your software versions when posting to support site). Below I'm using the devel version of tximport v1.15.8, but I believe this will be performing the same as release (v1.14), as the 8 version bumps were mostly documentation and modifications of warning messages.
Setup:
dir <- system.file("extdata", package="tximportData")
samples <- read.table(file.path(dir,"samples.txt"), header=TRUE)
files <- file.path(dir,"salmon_gibbs", samples$run, "quant.sf.gz")
names(files) <- paste0("sample",1:6)
With inferential replicates:
> txi <- tximport(files, type="salmon", txOut=TRUE)
> head(txi$counts)
sample1 sample2 sample3 sample4 sample5 sample6
ENST00000448914.1 0 0 0 0 0 0
ENST00000631435.1 0 0 0 0 0 0
ENST00000632684.1 0 0 0 0 0 0
ENST00000434970.2 0 0 0 0 0 0
ENST00000415118.1 0 0 0 0 0 0
ENST00000633010.1 0 0 0 0 0 0
Without inferential replicates:
txi <- tximport(files, type="salmon", txOut=TRUE, dropInfReps=TRUE)
> head(txi$counts)
sample1 sample2 sample3 sample4 sample5 sample6
ENST00000448914.1 0 0 0 0 0 0
ENST00000631435.1 0 0 0 0 0 0
ENST00000632684.1 0 0 0 0 0 0
ENST00000434970.2 0 0 0 0 0 0
ENST00000415118.1 0 0 0 0 0 0
ENST00000633010.1 0 0 0 0 0 0
Thank you for your reply! I'm using version 1.14.2
This happens not for txi$counts, but for txi$infReps. I tested with tximportData with the following command:
txi.inf.rep <- tximport(files, type = "salmon", txOut = TRUE, dropInfReps=FALSE, varReduce=FALSE)
For txi.inf.rep$counts, it's fine
sample1 sample2 sample3 sample4 sample5 sample6 ENST00000448914.1 0 0 0 0 0 0 ENST00000631435.1 0 0 0 0 0 0 ENST00000632684.1 0 0 0 0 0 0
But for txi.inf.rep$infReps, there's no tx name, only 1, 2, 3... as row names
sample1.1 sample1.2 sample1.3 sample1.4 sample1.5
1 0 0 0 0 0
2 0 0 0 0 0
3 0 0 0 0 0
The inferential bootstraps don't have rownames in storage, and for efficiency they are not named when imported with tximport, but kept as simple unnamed matrices (one per sample). The rows correspond to rownames(txi$counts).
The inferential information will be named in two cases though: (1) if you use varReduce=TRUE in tximport, the variance matrix is named, or otherwise, (2) you can use tximeta which will return the inferential replicate matrices as assays (one per inferential replicate).
The sample names on the matrices come directly from names(files), so you can fix it there.
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version 2.3.6
I do not exactly the answer but I am interested to know the answer of this question.
Were you able to try the code I posted?