getEnrich: Enrichment analysis for genes of network

In CeTF: Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

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)

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