Run_fGSEA_for_multiple_comparisons: Run GSEA analysis for multiple comparisons

In supatt-lab/SingCellaR: SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data

Run GSEA analysis for multiple comparisons

Description

Run GSEA analysis for multiple comparisons

Usage

Run_fGSEA_for_multiple_comparisons(
  GSEAPrerankedGenes_list,
  gmt.file = "",
  minSize = 5,
  maxSize = 2500,
  eps = 0,
  nPermSimple = 1000,
  n.seed = 1
)

Arguments

GSEAPrerankedGenes_list	The list of preranked genes.
gmt.file	The GMT file name.
minSize	The cutoff minimum number of genes in each gene set. Gene set that contains the number of genes lower than this number will be excluded. Default 5
maxSize	The cutoff maxiumum number of genes in each gene set. Gene set that contains the number of genes higher than this number will be excluded. Default 2500
eps	The eps paramenter for fgsea, this parameter sets the boundary for calculating the p value. Default 0
nPermSimple	The number of permutations in the simple fgsea implementation for preliminary estimation of P-values.
n.seed	The set seed number.
object	The SingCellaR object.

Value

a dataframe of GSEA analysis results.

supatt-lab/SingCellaR documentation built on Aug. 24, 2023, 5:49 p.m.