gseReactome {signatureSearch} | R Documentation

## Modified GSEA with Reactome

### Description

This modified Gene Set Enrichment Analysis (GSEA) of Reactome pathways supports gene test sets with large numbers of zeros.

### Usage

    gseReactome(
      geneList,
      organism = "human",
      exponent = 1,
      nPerm = 1000,
      minGSSize = 10,
      maxGSSize = 500,
      pvalueCutoff = 0.05,
      pAdjustMethod = "BH",
      verbose = TRUE,
      readable = FALSE
    )

### Arguments

`geneList` | order ranked geneList
`organism` | one of "human", "rat", "mouse", "celegans", "yeast", "zebrafish", "fly".
`exponent` | integer value used as exponent in GSEA algorithm.
`nPerm` | integer defining the number of permutation iterations for calculating p-values
`minGSSize` | minimal size of each geneSet for analyzing
`maxGSSize` | maximal size of each geneSet for analyzing
`pvalueCutoff` | pvalue Cutoff
`pAdjustMethod` | pvalue adjustment method
`verbose` | print message or not TRUE or FALSE indicating whether to convert gene Entrez ids to gene Symbols in the 'itemID' column in the FEA result table.
`readable` | TRUE or FALSE indicating whether to convert gene Entrez ids to gene Symbols in the 'itemID' column in the FEA result table.

### Value

feaResult object

### Examples

    # Gene Entrez id should be used for Reactome enrichment
    data(geneList, package="DOSE")
    #geneList[100:length(geneList)]=0
    #rc <- gseReactome(geneList=geneList, pvalueCutoff=1)

[Package signatureSearch version 1.6.3 Index]