fgsea_all: Run fgsea on all DESeq2 result tables

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Run fgsea on all DESeq2 result tables

Description

A wrapper for fgsea to convert ouput into tibbles

Usage

fgsea_all(res, gsets, FDR = 0.1, nperm = 10000, ...)

Arguments

res	A list of DESeq results
gsets	Gene sets
FDR	FDR cutoff, default 0.1
nperm	Number of permutations, default 10000
...	Additional options passed to fgsea

Value

A list of tibbles

Author(s)

Chris Stubben

Examples

## Not run: 
library(hciRdata)
fc <- write_gsea_rnk(res, write=FALSE)
x <- fgsea_all(fc, gsets=msig_pathways$KEGG)

## End(Not run)

HuntsmanCancerInstitute/hciR documentation built on Dec. 10, 2024, 12:22 p.m.