R: Extract functional terms enriched in the DE genes, based on...

topGOtable {pcaExplorer}

R Documentation

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
## Not run: 
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")

## End(Not run)

[Package pcaExplorer version 2.8.1 Index]