adjust fgsea.R script to changes in fgsea() function interface - Githubissues

snakemake-workflows / rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

MIT License

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adjust fgsea.R script to changes in fgsea() function interface #55

Closed dlaehnemann closed 2 years ago

dlaehnemann commented 2 years ago

Originally, the fgsea() function had an argument nperm= that determined the precision of p-value estimates. See for example this legacy documentation: https://bioconductor.org/packages/3.10/bioc/vignettes/fgsea/inst/doc/fgsea-tutorial.html

Starting with bioconductor 3.11, this precision is now directly specified via the eps= argument. See for example this version of the documentation: https://bioconductor.org/packages/3.11/bioc/vignettes/fgsea/inst/doc/fgsea-tutorial.html