prep_sc_DE_for_fgsea: Covert the ouptut of Seurat's FindMarkers to a table that...

In BrianLohman/SingleCellGarage: A collection of utilities to make working with (and combining) existing single cell packages easier

Description

This function assumes that a user has run Seurat's FindMarkers to assess differential expression between clusters and would like to next run GSEA with hciR's fgsea_all and gene to pathway data from hciRdata.

Usage

prep_sc_DE_for_fgsea(
  markers = markers,
  contrast = NULL,
  database = hciRdata::human100,
  human_homolog = FALSE,
  protein_coding = TRUE
)

Arguments

markers	Table from Seurat's FindMarkers
contrast	The name of the contrast
database	Table of genes to use when gathering annotations. Default is hciRdata::human100
human_homolog	Convert the gene names to human homologs. Default is FALSE

Examples

## Not run: 
sc_results = prep_sc_DE_for_fgsea(markers = markers, contrast = "cluster 4 vs. cluster 0")
fgsea_all(res = sc_results, gsets = msig_pathways$KEGG, FDR = 0.1, nperm = 10000)

## End(Not run)

BrianLohman/SingleCellGarage documentation built on Feb. 24, 2022, 4:58 a.m.