GeneOntology {enrichTF} | R Documentation

## Gene ontology enrichment analysis for provided gene list

### Description

User provide target gene list of forground region. This function will call function for gene ontology enrichment analysis

### Usage

    enrichGeneOntology(prevStep, inputTxt = NULL, outputTxt = NULL,
      outputPdf = NULL, orgDb = NULL, keyType = "SYMBOL", ...)

    ## S4 method for signature 'Step'
    enrichGeneOntology(prevStep, inputTxt = NULL,
      outputTxt = NULL, outputPdf = NULL, orgDb = NULL,
      keyType = "SYMBOL", ...)

    geneOntology(inputTxt, outputTxt = NULL, outputPdf = NULL,
      orgDb = NULL, keyType = "SYMBOL", ...)

### Arguments

`prevStep` | `Step-class` object scalar. This parameter is available when the upstream step function (printMap() to see the previous functions) have been sucessfully called. Accepted value can be the object return by any step function or be feed by `%>%` from last step function.
`inputTxt` | `Character` scalar. Gene list text file. All gene names are in one column.
`outputTxt` | `Character` scalar. Gene ontology enrichment analysis result table. Each row contain one gene ontology information.
`outputPdf` | `Character` scalar. Gene ontology enrichment analysis result figure. It contains gene ontology network.
`orgDb` | `Character` scalar. Bioconductor OrgDb object name for gene ontology enrichment analysis.
`keyType` | `Character` scalar. Gene name type include "SYMBOL" and "ENSEMBLE"
`...` | Additional arguments, currently unused.

### Details

Currently, this function call enrichGO from package clusterProfiler to implement this funtion.

### Value

An invisible `EnrichStep-class` object (`Step-class` based) scalar for downstream analysis.

### Author(s)

Zheng Wei

### See Also

`regionConnectTargetGene` `enrichRegionConnectTargetGene`

### Examples

    genelist.txt <- system.file(package = "enrichTF", "extdata","genelist.txt")
    geneOntology(inputTxt = genelist.txt, orgDb = "org.Hs.eg.db")

[Package enrichTF version 1.2.3 Index]