getGroupGO: Functional Profile of a gene set at specific GO level

Description Usage Arguments Value Examples

View source: R/getGroupGO.R

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

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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

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## 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)

CeTF documentation built on Nov. 25, 2020, 2 a.m.