enrichReactome {signatureSearch} | R Documentation

## Reactome Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enriched Reactome pathways with FDR control from hypergeometric test.

### Description

Reactome Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enriched Reactome pathways with FDR control from hypergeometric test.

### Usage

    enrichReactome(
      gene,
      organism = "human",
      pvalueCutoff = 0.05,
      pAdjustMethod = "BH",
      qvalueCutoff = 0.2,
      universe,
      minGSSize = 5,
      maxGSSize = 500,
      readable = FALSE
    )

### Arguments

`gene` | a vector of entrez gene id.
`organism` | one of "human", "rat", "mouse", "celegans", "yeast", "zebrafish", "fly".
`pvalueCutoff` | Cutoff value of pvalue.
`pAdjustMethod` | one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
`qvalueCutoff` | Cutoff value of qvalue
`universe` | background genes
`minGSSize` | minimal size of genes annotated by functional term for testing.
`maxGSSize` | maximal size of each gene set for analyzing
`readable` | TRUE or FALSE indicating whether to convert gene Entrez ids to gene Symbols in the 'itemID' column in the FEA result table.

### Value

A `feaResult` instance.

### See Also

`feaResult-class`

### Examples

    # This method supports duplicated elements in "gene"
    gene <- c(rep("4312",4), rep("8318",2), "991", "10874")
    #data(geneList, package="DOSE")
    #rc <- enrichReactome(gene=gene, universe=names(geneList))
    #result(rc)

[Package signatureSearch version 1.6.3 Index]