create_topGOdata-methods: Create topGOdata object for enrichment test with topGO...

In ViSEAGO: ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

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(), runfgsea()

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)

ViSEAGO documentation built on Nov. 8, 2020, 6:51 p.m.