Run_fGSEA_for_a_selected_cluster_vs_the_rest_of_clusters: Run GSEA analysis for a selected cluster vs the rest of...

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

Run GSEA analysis for a selected cluster vs the rest of clusters

Description

Run GSEA analysis for a selected cluster vs the rest of clusters

Usage

Run_fGSEA_for_a_selected_cluster_vs_the_rest_of_clusters(
  object,
  cluster.id = "",
  cluster.type = c("louvain", "walktrap", "kmeans", "merged_walktrap", "merged_louvain",
    "merged_kmeans"),
  diff.gene.method = "wilcoxon",
  gmt.file = "",
  fishers_exact_test = 0.1,
  plotGSEA = T,
  nTopGenesets = 10,
  minSize = 5,
  maxSize = 2500,
  eps = 0,
  nPermSimple = 1000
)

Arguments

object	The SingCellaR object.
cluster.id	The specified cluster id (e.g. 'cluster1').
cluster.type	The type of clustering method.
diff.gene.method	The method for differential gene expression analysis. Default 'wilcoxon'.
gmt.file	The GMT file name.
fishers_exact_test	The fisher's exact test cutoff p-value.
plotGSEA	is logical. If TRUE, this function will plot GSEA enrichment.
nTopGenesets	The number of showing top gene sets.
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.

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