getEnrich: Enrichment analysis for genes of network

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

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)

cbiagii/CeTF documentation built on Feb. 1, 2023, 3:19 p.m.