createGoMatrix: createGoMatrix

In robertsehlke/SETHRO: Simple Enrichment Testing for Highly Redundant Ontologies

Description

Using a bioconductor gene ontology annotation package, create a sparse binary matrix that maps gene identifiers (column names) to the GO terms they are annotated with (row names).

Usage

createGoMatrix(egGO2ALLEGS, min.genes = 5, max.genes = 300,
  excludeIEA = F)

Arguments

egGO2ALLEGS	GO to ALL identifiers mapping from any bioconductor annotation package. E.g. org.Dm.egGO2ALLEGS from the org.Dm.eg.db package.
min.genes	Minimum size of gene set to be considered, defaults to 5.
max.genes	Maximum size of gene set to be considered, defaults to 300.
excludeIEA

Author(s)

Robert Sehlke

Examples

## Not run: 
# example for annotation matrix creation
# may be used interchangably with createGoMatrix()
gomatrix = createAnnotationMatrix( list("GO:0000042"=paste0("gene",1:6),
                                           "GO:0000002"=paste0("gene",2:7),
                                           "GO:0000009"=paste0("gene",6:12)) )

# example call for main function
res = clusteredEnrichmentGO(gomatrix, 
                            geneset = paste0("gene",2:6),
                            universe = paste0("gene",1:12))

# example plot
plotClusteredEnrichment(res$results)

## End(Not run)

robertsehlke/SETHRO documentation built on May 29, 2019, 8:38 a.m.