pcaExplorer (version 1.0.2)

topGOtable: Extract functional terms enriched in the DE genes, based on topGO

Description

A wrapper for extracting functional GO terms enriched in the DE genes, based on the algorithm and the implementation in the topGO package

Usage

topGOtable(DEgenes, BGgenes, ontology = "BP", annot = annFUN.org,
  mapping = "org.Mm.eg.db", geneID = "symbol", topTablerows = 200,
  fullNamesInRows = TRUE, addGeneToTerms = TRUE, plotGraph = FALSE,
  plotNodes = 10, writeOutput = FALSE, outputFile = "")

Arguments

DEgenes

A vector of (differentially expressed) genes

BGgenes

A vector of background genes, e.g. all (expressed) genes in the assays

ontology

Which Gene Ontology domain to analyze: BP (Biological Process), MF (Molecular Function), or CC (Cellular Component)

annot

Which function to use for annotating genes to GO terms. Defaults to annFUN.org

mapping

Which org.XX.eg.db to use for annotation - select according to the species

geneID

Which format the genes are provided. Defaults to symbol, could also be entrez or ENSEMBL

topTablerows

How many rows to report before any filtering

fullNamesInRows

Logical, whether to display or not the full names for the GO terms

addGeneToTerms

Logical, whether to add a column with all genes annotated to each GO term

plotGraph

Logical, if TRUE additionally plots a graph on the identified GO terms

plotNodes

Number of nodes to plot

writeOutput

Logical, if TRUE additionally writes out the result to a file

outputFile

Name of the file the result should be written into

Value

• A table containing the computed GO Terms and related enrichment scores

Examples

library(airway)
library(DESeq2)
data(airway)
airway
dds_airway <- DESeqDataSet(airway, design= ~ cell + dex)

# Example, performing extraction of enriched functional categories in
# detected significantly expressed genes

dds_airway <- DESeq(dds_airway)
res_airway <- results(dds_airway)
library("AnnotationDbi")
library("org.Hs.eg.db")
res_airway$symbol <- mapIds(org.Hs.eg.db,
                            keys=row.names(res_airway),
                            column="SYMBOL",
                            keytype="ENSEMBL",
                            multiVals="first")
res_airway$entrez <- mapIds(org.Hs.eg.db,
                            keys=row.names(res_airway),
                            column="ENTREZID",
                            keytype="ENSEMBL",
                            multiVals="first")
resOrdered <- as.data.frame(res_airway[order(res_airway$padj),])
de_df <- resOrdered[resOrdered$padj < .05 & !is.na(resOrdered$padj),]
de_symbols <- de_df$symbol
bg_ids <- rownames(dds_airway)[rowSums(counts(dds_airway)) > 0]
bg_symbols <- mapIds(org.Hs.eg.db,
                     keys=bg_ids,
                     column="SYMBOL",
                     keytype="ENSEMBL",
                     multiVals="first")
library(topGO)

topgoDE_airway <- topGOtable(de_symbols, bg_symbols,
                             ontology = "BP",
                             mapping = "org.Hs.eg.db",
                             geneID = "symbol")