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markziemann / mitch

An R package for multi-dimensional pathway enrichment analysis
https://bioconductor.org/packages/mitch
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gmt_import problem with empty lines #19

Closed markziemann closed 7 months ago

markziemann commented 4 years ago

If the GMT file contains empty lines it creates empty gene sets.

[126] "SRP102542: Genes expressed differentially in old people who do resistance training: downregulated"
[127] ""
[128] "SRP101810: bulk-cell RNA-seq of anti-CD3 anti-CD28 monoclonal antibodies stimulated T cell clone versus GAD peptide-loaded tetramer stimulated T cell clone: downregulated"

The solution is to remove empty lines as they are read in

markziemann commented 4 years ago

Something like this should be sufficient

diab <- diab[which(!names(diab)=='')]