Question

Htseq files import via tximport

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sally.badawi • 0

@sallybadawi-16174

Last seen 5.8 years ago

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 • 2.2k views

ADD COMMENT • link updated 5.8 years ago by Michael Love 42k • written 5.8 years ago by sally.badawi • 0

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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 REPLY • link updated 5.8 years ago by Martin Morgan 25k • written 5.8 years ago by sally.badawi • 0

score 0 · Answer 1 · 2019-02-19

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Michael Love 42k

@mikelove

Last seen 32 minutes ago

United States

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 COMMENT • link 5.8 years ago Michael Love 42k

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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 REPLY • link 5.8 years ago sally.badawi • 0

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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 REPLY • link 5.8 years ago Michael Love 42k