getEnrich {CeTF} | R Documentation

## Enrichment analysis for genes of network

### Description

Enrichment analysis of a set of genes derived from the network of any condition using WebGestalt interface in R. Given a vector of genes, this function will return the enrichment related to the selected database.

### Usage

    getEnrich(
      organism,
      database,
      genes,
      refGene,
      GeneType,
      fdrMethod = "BH",
      fdrThr = 0.05,
      minNum = 5,
      maxNum = 500
    )

### Arguments

`organism` | WebGestaltR supports 12 organisms. Users can use the function listOrganism() to check available organisms.
`database` | The functional categories for the enrichment analysis. Users can use the function listGeneSet() to check the available functional databases for the selected organism. Multiple databases in a vector are supported too.
`genes` | Should be an R vector object containing the interesting gene list.
`refGene` | Should be an R vector object containing the reference gene list. There is a list with reference genes for 5 organisms in this package (see `refGenes`).
`GeneType` | The ID type of the genes and refGene (they must be the same type). Users can use the function listIdType() to check the available gene types.
`fdrMethod` | Has five FDR methods: holm, hochberg, hommel, bonferroni, BH and BY (default: BH).
`fdrThr` | The significant threshold for fdrMethod (default: 0.05).
`minNum` | Will be exclude the categories with the number of annotated genes less than minNum for enrichment analysis (default: 5).
`maxNum` | Will be exclude the categories with the number of annotated genes larger than maxNum for enrichment analysis (default: 500).

### Value

Returns an list with the results of the enrichment analysis of the genes and a network with the database ID (column 1) and the corresponding genes (column 2).

### Examples

    ## Not run:
    # load the CeTF class object resulted from runAnalysis function
    data(CeTFdemo)

    # getting the genes in network of condition 1
    genes <- unique(c(as.character(NetworkData(CeTFdemo, 'network1')[, 'gene1']),
                     as.character(NetworkData(CeTFdemo, 'network1')[, 'gene2'])))

    # performing getEnrich analysis
    cond1 <- getEnrich(organism='hsapiens', database='geneontology_Biological_Process',
                       genes=genes, GeneType='ensembl_gene_id',
                       refGene=refGenes$Homo_sapiens$ENSEMBL,
                       fdrMethod = 'BH', fdrThr = 0.05, minNum = 5, maxNum = 500)

    ## End(Not run)

[Package CeTF version 1.2.4 Index]