runCamera: Function to run enrichment analysis using Camera from LIMMA
In lujunyan1118/jyluMisc: Handy functions for CLL project

runCamera

R Documentation

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.