Question: Htseq files import via tximport
0
gravatar for sally.badawi
8 weeks ago by
sally.badawi0 wrote:

Good morning,

Ive been trying to import htseq files into tximport to transform count reads from transcripts to gene level, All files exist in directory. I am facing this error: txi <- tximport(files, type = "none", geneIdCol = "UCSCID", countsCol = "Counts") reading in files with readtsv 1 Error in importer(files[i]) : could not find function "importer"

I tried different things, changing file format, unistalling and re-installing tximport package, but Im still having this error!

Any help with this?

Thank you,

tximport importer • 96 views
ADD COMMENTlink modified 8 weeks ago by Michael Love22k • written 8 weeks ago by sally.badawi0

If I try another option:

sampleFiles <- grep("S",list.files(dir),value=TRUE)
> txi <- tximport(sampleFiles, type = "none", geneIdCol = "UCSC_ID", countsCol = "Counts")
Error in tximport(sampleFiles, type = "none", geneIdCol = "UCSC_ID", countsCol = "Counts") : 
  all(file.exists(files)) is not TRUE
> all(file.exists(files))
[1] TRUE

I get another error, I dont know where its coming from.

Thank you for yor help

ADD REPLYlink written 8 weeks ago by sally.badawi0
Answer: Htseq files import via tximport
0
gravatar for Michael Love
8 weeks ago by
Michael Love22k
United States
Michael Love22k wrote:

tximport is for importing from transcript abundance software, please refer to ?tximport to see what types are supported. We have a specific importer in DESeq2 for htseq, see the workflow or vignette for details.

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by Michael Love22k

Cant I obtain gene level counts (I already have transcripts counts) from the htseq files I have? Or originally counts should be read as genes in the htseq algorithm. If yes, any proposed function to do this? SummarizetoGene function also require a tximport file. Thank you

ADD REPLYlink written 8 weeks ago by sally.badawi0

Please read the workflow and documentation in general before posting additional questions. We talk about how to bring in counts from htseq in the workflow. Yes htseq creates gene level counts and we have dedicated functions to import these files as I’ve already said.

ADD REPLYlink written 8 weeks ago by Michael Love22k
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