perform_fgsea: A function that will perform fgsea analysis on all cells in a...

In FloWuenne/scFunctions: Functions for single cell data analysis

Description

A function that will perform fgsea analysis on all cells in a given Seurat object.

Usage

perform_fgsea(
  seurat_object,
  cell_types = sort(unique(seurat_object@ident)),
  output_dir = ".",
  pathway_file
)

Arguments

seurat_object	The S4 Seurat object which contains filtered and normalized cells in the data slot.
output_dir	The relative directory that will be used to save results.
de_groups	The two group labels to use for differential expression, supplied as a vector.
clusters_to_exclude	Define a vector of clusters for which you don't want to perform DE analysis.

Examples

DE_Seurat()

FloWuenne/scFunctions documentation built on June 3, 2021, 6:42 p.m.