getGroupGO {CeTF} | R Documentation

## Functional Profile of a gene set at specific GO level

### Description

Functional Profile of a gene set at specific GO level. Given a vector of genes, this function will return the GO profile at a specific level.

### Usage

    getGroupGO(genes, ont = "BP", keyType, annoPkg, level = 3)

### Arguments

`genes` | Character vector with the genes to perform the functional profile.
`ont` | One of 'MF', 'BP', and 'CC' subontologies (default: 'BP').
`keyType` | Key type of inputted genes (i.e. 'ENSEMBL', 'SYMBOL', 'ENTREZID').
`annoPkg` | Package of annotation of specific organism (i.e. org.Hs.eg.db, org.Bt.eg.db, org.Rn.eg.db, etc).
`level` | Specific GO Level (default: 3).

### Value

Returns an list with the results of the functional profile of the genes and a network with the ontologies (column 1) and the corresponding genes (column 2).

### Examples

    ## Not run:
    # load the annotation package
    library(org.Hs.eg.db)

    # 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 getGroupGO analysis
    cond1 <- getGroupGO(genes = genes,
                        ont = 'BP',
                        keyType = 'ENSEMBL',
                        annoPkg = org.Hs.eg.db,
                        level = 3)

    ## End(Not run)

[Package CeTF version 1.6.0 Index]