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

In federicomarini/pcaExplorer: Interactive Visualization of RNA-seq Data Using a Principal Components Approach

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 = "",
  topGO_method2 = "elim",
  do_padj = FALSE
)

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
topGO_method2	Character, specifying which of the methods implemented by topGO should be used, in addition to the classic algorithm. Defaults to elim
do_padj	Logical, whether to perform the adjustment on the p-values from the specific topGO method, based on the FDR correction. Defaults to FALSE, since the assumption of independent hypotheses is somewhat violated by the intrinsic DAG-structure of the Gene Ontology Terms

Details

Allowed values assumed by the topGO_method2 parameter are one of the following: elim, weight, weight01, lea, parentchild. For more details on this, please refer to the original documentation of the topGO package itself

Value

A table containing the computed GO Terms and related enrichment scores

Examples

library("airway")
library("DESeq2")
data("airway", package = "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)

federicomarini/pcaExplorer documentation built on Sept. 29, 2024, 9:31 p.m.