aSwitchList error

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kris r

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Mar 14, 2023, 4:45:37 PM3/14/23

to IsoformSwitchAnalyzeR

Hello!

I am attempting to run analysis with this tool but running into an issue when creating the aSwitchList.

I'm using salmon output with gencode gtf and when I run the command:

aSwitchList <- importRdata(
isoformCountMatrix = salmonQuant$counts,
isoformRepExpression = salmonQuant$abundance,
designMatrix = myDesign,
isoformExonAnnoation = "/Users/xx/GenomeFiles/gencode.v40.primary_assembly.annotation.gtf",
#isoformNtFasta = "/Users/xx/GenomeFiles/xx.fa",
fixStringTieAnnotationProblem = F,
showProgress = F
)

it stops with the following error:

Step 1 of 7: Checking data...
Step 2 of 7: Obtaining annotation...
importing GTF (this may take a while)...
Error in dplyr::full_join():
! ... must be empty.
✖ Problematic argument:
• all = TRUE

some info on the env:
sessionInfo()
R version 4.1.3 (2022-03-10)

dplyr_1.1.0
tidyverse_2.0.0
IsoformSwitchAnalyzeR_1.16.0

Any idea on what this could be?

Thanks!

Kristoffer Vitting-Seerup

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Mar 15, 2023, 12:48:02 AM3/15/23

to IsoformSwitchAnalyzeR

You just need to upgrade to the newest version from github :-)

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