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 = "",
      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)
    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 2.14.2 Index]