Question

tximport importer isoform abundance

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Ina Hoeschele ▴ 620

@ina-hoeschele-2992

Last seen 3.3 years ago

United States

Hi, I am trying to run tximport on stringtie ctab files but am getting the error message below. I cannot find any documentation for the importer argument - what are the allowed values? Please do not tell me to use the latest R, I am using an HPC cluster where I do not have control over the R version, R 3.6.0 is the latest R I was able to convince the sys admin to install. It looks like for my version importer does not yet default to readr (tsv)? Thanks, Ina

txi.list <- tximport(files=flist,countsFromAbundance="lengthScaledTPM",tx2gene=tx2gene,readLength=150) reading in files with readtsv 1 Error in importer(files[i]) : could not find function "importer" ?tximport sessionInfo() R version 3.6.0 (2019-04-26) Platform: x8664-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /apps/easybuild/software/haswell-haswell/OpenBLAS/0.3.5-GCC-8.2.0-2.31.1/lib/libopenblas_haswellp-r0.3.5.so

locale: [1] LCCTYPE=enUS.UTF-8 LCNUMERIC=C [3] LCTIME=enUS.UTF-8 LCCOLLATE=enUS.UTF-8 [5] LCMONETARY=enUS.UTF-8 LCMESSAGES=enUS.UTF-8 [7] LCPAPER=enUS.UTF-8 LCNAME=C [9] LCADDRESS=C LCTELEPHONE=C [11] LCMEASUREMENT=enUS.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] tximport_1.12.3

loaded via a namespace (and not attached): [1] readr1.3.1 compiler3.6.0 R62.4.0 hms0.4.2 [5] tools3.6.0 pillar1.4.1 tibble2.1.3 Rcpp1.0.1 [9] crayon1.3.4 pkgconfig2.0.2 rlang_0.3.4

tximport • 1.5k views

ADD COMMENT • link updated 19 months ago by tangming2005 ▴ 200 • written 4.5 years ago by Ina Hoeschele ▴ 620

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I had the same error today.

specify type == "none" and importer = read_tsv worked for me

tximport(files, tx2gene = tx2gene, type = "none", ignoreAfterBar = F, txIdCol = "gene_name", geneIdCol = "gene", abundanceCol = "abundance", countsCol = "counts", lengthCol = "length", importer = read_tsv)

ADD REPLY • link 19 months ago tangming2005 ▴ 200

score 0 · Answer 1 · 2020-06-22

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Michael Love 43k

@mikelove

Last seen 23 hours ago

United States

For help with a specific function, first see ?tximport.

In particular note the type argument listed there.

There is also a code chunk for StringTie in the tximport vignette.

ADD COMMENT • link 4.5 years ago Michael Love 43k

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Thank you and I am embarrassed, I had of course meant to add type=”stringtie” but overlooked that it was not there. I have a few questions about the output (for txOut=FALSE).

The first list element is an abundance matrix, but it is not clear to me what abundance means at the gene level (Stringtie’s coverage values summed over transcripts of the same gene?)?

The second list element is a count matrix, is it computed from Stringtie’s coverage values which are converted to transcript TPMs (because I set countsFromAbundance="lengthScaledTPM") and then summed across transcripts of the same gene?

In addition to the gene-based values, I also need counts (not TPM) for the individual transcripts. Can I get these by setting txOut=TRUE and countsFromAbundance=”no”?

ADD REPLY • link 4.5 years ago Ina Hoeschele ▴ 620

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The abundance is summed from the transcripts to the gene level. It's the simple sum of the transcript abundances.

Yes, that is what lengthScaledTPM does for StringTie input.

Yes.

ADD REPLY • link 4.5 years ago Michael Love 43k