topGOtable {pcaExplorer} | R Documentation |
A wrapper for extracting functional GO terms enriched in the DE genes, based on the algorithm and the implementation in the topGO package
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 = "")
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: |
annot |
Which function to use for annotating genes to GO terms. Defaults to |
mapping |
Which |
geneID |
Which format the genes are provided. Defaults to |
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 |
A table containing the computed GO Terms and related enrichment scores
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)