goseqTable {ideal} | R Documentation

## Extract functional terms enriched in the DE genes, based on goseq

### Description

A wrapper for extracting functional GO terms enriched in a list of (DE) genes, based on the algorithm and the implementation in the goseq package

### Usage

    goseqTable(
      de.genes,
      assayed.genes,
      genome = "hg38",
      id = "ensGene",
      testCats = c("GO:BP", "GO:MF", "GO:CC"),
      FDR_GO_cutoff = 1,
      nTop = 200,
      orgDbPkg = "org.Hs.eg.db",
      addGeneToTerms = TRUE
    )

### Arguments

`de.genes` | A vector of (differentially expressed) genes
`assayed.genes` | A vector of background genes, e.g. all (expressed) genes in the assays
`genome` | A string identifying the genome that genes refer to, as in the `goseq` function
`id` | A string identifying the gene identifier used by genes, as in the `goseq` function
`testCats` | A vector specifying which categories to test for over representation amongst DE genes - can be any combination of "GO:CC", "GO:BP", "GO:MF" & "KEGG"
`FDR_GO_cutoff` | Numeric value for subsetting the results
`nTop` | Number of categories to extract, and optionally process for adding genes to the respective
`orgDbPkg` | Character string, named as the `org.XX.eg.db` package which should be available in Bioconductor
`addGeneToTerms` | Logical, whether to add a column with all genes annotated to each GO term

### Details

Note: the feature length retrieval is based on the `goseq` function, and requires that the corresponding TxDb packages are installed and available

### Value

A table containing the computed GO Terms and related enrichment scores

### Examples

    library(airway)
    data(airway)
    airway
    dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),
                                                 colData = colData(airway),
                                                 design=~cell+dex)
    dds_airway <- DESeq2::DESeq(dds_airway)
    res_airway <- DESeq2::results(dds_airway)

    res_subset <- deseqresult2DEgenes(res_airway)[1:100,]
    myde <- res_subset$id
    myassayed <- rownames(res_airway)

    ## Not run:
    mygo <- goseqTable(myde,
                       myassayed,
                       testCats = "GO:BP",
                       addGeneToTerms = FALSE)
    head(mygo)

    ## End(Not run)

[Package ideal version 1.11.2 Index]