createAnnotationMatrix: createAnnotationMatrix

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

Description

From a list of annotations, create a sparse binary matrix that maps gene identifiers (column names) to the GO terms they are annotated with (row names).

Usage

createAnnotationMatrix(annotationlist, min.genes = 5, max.genes = 300)

Arguments

annotationlist	Named list of character vectors. Names are assumed to be gene set identifiers, character vectors member gene identifiers.
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.

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.