create_topGOdata {ViSEAGO} | R Documentation

## Create topGOdata object for enrichment test with topGO package.

### Description

This method create a `topGOdata-class` object required by topGO package in order to perform GO enrichment test.

### Usage

    create_topGOdata(geneSel, allGenes, geneList = NULL, gene2GO, ont,
      nodeSize)

      ## S4 method for signature 'ANY,ANY,ANY,gene2GO,character,numeric'
    create_topGOdata(geneSel,
      allGenes, geneList = NULL, gene2GO, ont, nodeSize)

### Arguments

`geneSel` | genes of interest.
`allGenes` | customized background genes.
`geneList` | logical factor (1: genes of interest, 0: genes background, and gene identifiants in `names`) (default value to NULL).
`gene2GO` | a `gene2GO-class` object created by `annotate` method.
`ont` | the ontology used is "MF" (Molecuar Function), "BP" (Biological Process), or "CC" (Cellular Component).
`nodeSize` | the minimum number of genes for each GO term.

### Details

This method is a convenient wrapper building a `topGOdata-class` object using a given ontology category (`ont` argument) in order to perform GO enrichment test. The complete GO annotation is required (`gene2GO` argument) and also the list of genes of interest (`geneSel` argument) against the corresponding background (`allGenes` argument) separately, or grouped together in a `factor` (`geneList` argument).

### Value

a `topGOdata-class` object required by `runTest` from topGO package.

### References

Alexa A, Rahnenfuhrer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 2006; 22:1600-1607.

### See Also

Other GO_terms: `GOcount`, `GOterms_heatmap`, `annotate`, `gene2GO-class`, `merge_enrich_terms`

### Examples

     ###################
     # load genes identifiants (GeneID,ENS...) background (Expressed genes)
     background<-scan(
      system.file(
       "extdata/data/input",
       "background_L.txt",
       package = "ViSEAGO"
      ),
      quiet=TRUE,
      what=""
     )

     ###################
     # load Differentialy Expressed (DE) gene identifiants from files
     pregnantvslactateDE<-scan(
      system.file(
       "extdata/data/input",
       "pregnantvslactateDE.txt",
       package = "ViSEAGO"
     ),
      quiet=TRUE,
      what=""
     )
    ## Not run:
    ###################
    # create topGOdata for BP for each list of DE genes
    BP_L_pregnantvslactate<-ViSEAGO::create_topGOdata(
     geneSel=pregnantvslactateDE,
     allGenes=background,
     gene2GO=myGENE2GO,
     ont="BP",
     nodeSize=5
    )

    ## End(Not run)

[Package ViSEAGO version 1.0.0 Index]