runCamera: Function to run enrichment analysis using Camera from LIMMA

In lujunyan1118/jyluMisc: Handy functions for CLL project

Function to run enrichment analysis using Camera from LIMMA

Description

A funtion to perform gene enrichment analysis using rotational test (fry or camera) implemented in limma package.

Usage

runCamera(
  exprMat,
  design,
  gmtFile,
  id = NULL,
  contrast = ncol(design),
  method = "camera",
  pCut = 0.05,
  ifFDR = FALSE,
  removePrefix = NULL,
  plotTitle = "",
  insideLegend = FALSE
)

Arguments

exprMat	Gene expression matrix. Genes as rows and samples as columns.
design	Design matrix as used by limma.
gmtFile	A path to the gene signature file.
id	A character vector of identifiers for genes used in the gmt file, ff the row names are not the same as the identfiers in the gmt file.
contrast	The index of the colum in design matrix that should be used as contrast for enrichment analysis. Default is the last column.
method	Wheter using "camera" (competitive) or "fry" (self-contained) method
pCut	Cut-off for significance of enrichment.
removePrefix	Remove a certain string in the set names to make them shorter. For example, "HALLMARK_".
plotTitle	The tilte used for enrichment bar plot.
ifDFR	Whether raw p value or adjusted p value (FDR) should be used for significance cut-off
insideLegned	Whether to put the legend inside the bar plot to save space.

lujunyan1118/jyluMisc documentation built on Jan. 21, 2025, 2:18 p.m.