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 clusterProfiler. Given a vector of genes, this function will return the enrichment related to the selected database.

### Usage

    getEnrich(
      genes,
      organismDB,
      keyType,
      ont,
      fdrMethod = "BH",
      fdrThr = 0.05,
      minGSSize = 5,
      maxGSSize = 500
    )

### Arguments

`genes` | Should be an R vector object containing the interesting gene list.
`organismDB` | clusterProfiler supports a lot of different organisms. Users can check the following link (https://www.bioconductor.org/packages/release/data/annotation/) and search for annotations starting with *org.*.
`keyType` | The ID type of the input genes (i.e. SYMBOL, ENTREZID, ENSEMBL, etc.).
`ont` | The functional categories for the enrichment analysis. The available ontologies are Biological Process (BP), Molecular Function (MF) and Cellular Component (CC).
`fdrMethod` | Has five FDR methods: holm, hochberg, hommel, bonferroni, BH, BY, fdr and none(default: BH).
`fdrThr` | The significant threshold for selected pathways (default: 0.05).
`minGSSize` | Will be exclude the categories with the number of annotated genes less than minGSSize for enrichment analysis (default: 5).
`maxGSSize` | Will be exclude the categories with the number of annotated genes larger than maxGSSize 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
    library(org.Hs.eg.db)
    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(genes = genes, organismDB = org.Hs.eg.db, keyType = 'ENSEMBL',
                       ont = 'BP', fdrMethod = "BH", fdrThr = 0.05, minGSSize = 5,
                       maxGSSize = 500)

    ## End(Not run)

[Package CeTF version 1.6.0 Index]