Question: there is no "tx2gene.gencode.v27.csv" in tximportData
0
gravatar for krwyaong.ju
13 months ago by
krwyaong.ju0 wrote:

as installed tximportData, there was no "tx2gene.gencode.v27.csv".

below is the shell for installation;

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
> biocLite("tximportData")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4 (2018-03-15).
Installing package(s) ‘tximportData’
trying URL 'https://bioconductor.org/packages/3.6/data/experiment/src/contrib/tximportData_1.6.0.tar.gz'
Content type 'application/x-gzip' length 109001249 bytes (104.0 MB)
==================================================
downloaded 104.0 MB

* installing *source* package ‘tximportData’ ...
** inst
** help
No man pages found in package  ‘tximportData’
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (tximportData)

The downloaded source packages are in
    ‘/tmp/RtmpYT5Qzw/downloaded_packages’
> library(tximportData)
> dir <- system.file("extdata", package = "tximportData")
> list.files(dir)
 [1] "cufflinks"            "kallisto"             "kallisto_boot"       
 [4] "rsem"                 "sailfish"             "salmon"              
 [7] "salmon_gibbs"         "samples_extended.txt" "samples.txt"         
[10] "tx2gene.csv"         
>

tximport • 506 views
ADD COMMENTlink modified 13 months ago by Michael Love24k • written 13 months ago by krwyaong.ju0
Answer: there is no "tx2gene.gencode.v27.csv" in tximportData
0
gravatar for Michael Love
13 months ago by
Michael Love24k
United States
Michael Love24k wrote:

Make sure to always post your sessionInfo(). In this case, you are using an older version of tximport and tximportData than appear on the Bioconductor website. Check the Session Info section of the current vignette and compare with your own sessionInfo():

https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#session-info

ADD COMMENTlink written 13 months ago by Michael Love24k
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