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To The Developers,
I updated my R from version 3.3.2 to version 3.4.1 primarily so I can use the latest version of DESeq2 which is version 1.16.1
I'm using the tximport package to import transcript-level estimates. It was working before when I'm using R version 3.3.2 and version 3.3.2 but my DESeq2 version is still 1.14.1 so I decided to update my R version.
Upon running the tximport command "tx.all <- tximport(myfiles, type = "salmon", tx2gene = tx2gene, reader = read_tsv)" on R version 3.4.1 im getting an error whihc is "unused argument: reader = read_tsv"
How can I get this to work on R version 3.4.1?
Please and kindly advise.
Sincerely,
Asher
Did you re-install tximport after your R upgrade? If so, what is the output of `sessionInfo()`? If not, you should reinstall all your Bioconductor packages after the upgrade of R and then retry.
Check also BiocInstaller::biocValid() which will indicate out-of-date packages for your version BiocInstaller::biocVersion() of Bioconductor.
To The Developers,
I did re-install the R version 3.4.1. I did re-install the DESeq2 version 1.16.1 and tximport version 1.4.0 through the Bioconductor page as reflected on the session info below.
However, I'm still getting the same error when running this command.
> tx.all <- tximport(myfiles, type = "salmon", tx2gene = tx2gene, reader = read_tsv)
Error in tximport(myfiles, type = "salmon", tx2gene = tx2gene, reader = read_tsv) :
unused argument (reader = read_tsv)
Again, I've never encountered this error on R version 3.3.2 and 3.3.3.
s
Please advise.
Session Info:
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] readr_1.1.1 tximport_1.4.0 genefilter_1.58.1
[4] pheatmap_1.0.8 RColorBrewer_1.1-2 ggplot2_2.2.1
[7] gplots_3.0.1 DESeq2_1.16.1 SummarizedExperiment_1.6.3
[10] DelayedArray_0.2.7 matrixStats_0.52.2 Biobase_2.36.2
[13] GenomicRanges_1.28.4 GenomeInfoDb_1.12.2 IRanges_2.10.2
[16] S4Vectors_0.14.3 BiocGenerics_0.22.0 BiocInstaller_1.26.0
loaded via a namespace (and not attached):
[1] bit64_0.9-7 splines_3.4.1 gtools_3.5.0
[4] Formula_1.2-2 latticeExtra_0.6-28 blob_1.1.0
[7] GenomeInfoDbData_0.99.0 RSQLite_2.0 backports_1.1.0
[10] lattice_0.20-35 digest_0.6.12 XVector_0.16.0
[13] checkmate_1.8.3 colorspace_1.3-2 htmltools_0.3.6
[16] Matrix_1.2-10 plyr_1.8.4 XML_3.98-1.9
[19] zlibbioc_1.22.0 xtable_1.8-2 scales_0.4.1
[22] gdata_2.18.0 BiocParallel_1.10.1 htmlTable_1.9
[25] tibble_1.3.3 annotate_1.54.0 nnet_7.3-12
[28] lazyeval_0.2.0 survival_2.41-3 magrittr_1.5
[31] memoise_1.1.0 foreign_0.8-69 tools_3.4.1
[34] data.table_1.10.4 hms_0.3 stringr_1.2.0
[37] munsell_0.4.3 locfit_1.5-9.1 cluster_2.0.6
Your version of tximport doesn't have that argument. Please see ?tximport as I said previously
Hi Michael,
I would like to still use that argument as that's what works for me before on the previous R version.
What version of tximport should I use for me to be able to use that argument again? And can I used that old version with the new version of R and Bioconductor that I installed?
Thanks and best regards,
Asher
From the tximport vignette:
Note: While tximport works without any dependencies, it is significantly faster to read in files using the readr package. If tximport detects that readr is installed, then it will use the
readr::read_tsvfunction by default. A change from version 1.2 to 1.4 is that the reader is not specified by the user anymore, but chosen automatically based on the availability of the readr package. Advanced users can still customize the import of files using theimporterargument.This was also in the NEWS file, where you can go to find out about changes to the software:
o Removing 'reader' argument, leaving only 'importer' argument. In addition, read_tsv will be used by default if readr package is installed.Hi Michael,
Dumb follow-up question here, I have a readr package installed (version 1.1.1) when I upgraded my R version to 3.4.1. Saying that "read_tsv will be used by default if readr package is installed" is for the older tximport version (1.2.0) and not for version 1.4.0? Because since I upgraded my R version and the tximport version also, the readr argument is not there.
What I'm trying to show you is that you have all the answers on your machine.
You can type vignette("tximport") and news(package="tximport") in R, and find the relevant information for the version of software you have installed. So the answer to, when did this change happen, is in those documents. You can use packageVersion() and sessionInfo() to confirm which version you have. I'm writing this reply in a general way, so that the information is useful and appropriate for anyone who is reading this.
Note that you can just run tximport() and if readr is installed, and you have the current version of tximport, the function will tell you that it is using readr::read_tsv.