msigdb_gsea {GenomicSuperSignature}R Documentation

MSigDB GSEA results

Description

MSigDB GSEA results

Usage

msigdb_gsea(
  ind,
  RAVmodel,
  category = "C2",
  n = NULL,
  pvalueCutoff = 0.5,
  minGSSize = 10,
  maxGSSize = 500,
  pAdjustMethod = "BH",
  verbose = FALSE,
  seed = FALSE,
  by = "fgsea",
  geneSets = NULL
)

Arguments

ind

An interger. Index of RAV to apply GSEA.

RAVmodel

PCAGenomicSignature object.

category

A character vector representing MSigDB category. Options are "H", "C1", "C2"(default), "C3", "C4", "C5", "C6", and "C7"

n

An interger. The number of top and bottom enriched pathways to plot. Default is NULL, which prints out all the pathways enriched under pvalueCutoff.

pvalueCutoff

Cutoff for both pvalue and p.adjust. Default is 0.5.

minGSSize

A mininum size of gene set to be analyzed

maxGSSize

A maximum size of gene set to be analyzed

pAdjustMethod

p-value adjustment methods, which will be used as an input for method argument of p.adjust function. Available options are "holm", "hochberg", "hommel", "bonferroni", "BH"(default), "BY", "fdr", "none".

verbose

Logical. Default is FALSE.

seed

Logical. Default is FALSE.

by

Available options are c("fgsea", "DOSE"). Default "fgsea".

geneSets

Custom genesets to use with MSigDB genesets. It should be in a named list format.

Value

Barplot of GSEA output. Top and bottom n genesets based on NES are plotted and qvalues are denoted by color.


[Package GenomicSuperSignature version 1.2.0 Index]