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BaderLab / Tempora

Pathway-based trajectory inference method for time-series scRNAseq data
MIT License
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Error in CalculatePWProfiles due to GSEABase::getGmt #22

Closed zandigohar closed 2 years ago

zandigohar commented 2 years ago

To estimate pathway enrichment profiles of clusters, I was trying to run CalculatePWProfiles on a dataset and got into an error.

After reading the R code in CalculatePWProfiles, I realized the actual issue is with pathwaygmt <- GSEABase::getGmt(gmt_file, sep = "\t") which apparently does not have anything to do with a user's input data.

The screenshot of my console, including the GSEA version, gmt file name, and the error message is as below:

image

R version 4.1.3 (2022-03-10) Platform: x86_64-conda-linux-gnu (64-bit)

Are there any workarounds for this? I highly appreciate any help.

zandigohar commented 2 years ago

I downloaded an earlier version of gmt file (May 5th instead of May 12th) and it worked! So I am closing this. Not sure why the latest version throws issues.

risserlin commented 2 years ago

Thanks for reporting. It looks like there are a bunch of pathways coming from some of the databases that don't have names and the paxtools parser is giving them all the name "OTHER".