attract (version 1.24.0)

buildKeggIncidenceMatrix: Internal function - buildings the KEGG incidence matrix requird by GSEAlm.

Description

Internal function - buildings the KEGG incidence matrix requird by GSEAlm.

Usage

buildKeggIncidenceMatrix(kegg.ids, gene.ids, annotation, database, analysis, envPos)

Arguments

kegg.ids

character vector of KEGG pathway ids.

gene.ids

character vector of gene ids.

annotation

character string that denotes which annotation package to be used, eg. illuminaHumanv1.db.

database

a character string specifiying what pathway database you would like to use.

analysis

a character string specifying what type of experiment you performed, microarray or RNAseq.

envPos

the position of the annotation package in the R search path.

Value

A matrix object with 0 and 1 entries where 1 denotes membership of a gene in a KEGG or reactome pathway, 0 denotes non-membership.

Details

This function is called internally by findAttractors.

References

Kanehisa, M. and S. Goto, KEGG: Kyoto Encyclopedia of Genes and Genomes. . Nucleic Acids Res., 2000. 28: p. 27-30.

Examples

## Not run: 
# # this takes a long time!
# require("illuminaHumanv2.db", character.only=TRUE)
# loadNamespace("illuminaHumanv2.db")
# envPos <- match(paste("package:", "illuminaHumanv2.db", sep=""), search())
# kegg.ids <- ls(illuminaHumanv2PATH2PROBE) 
# gene.ids <- ls(illuminaHumanv2PATH)
# database <-"KEGG"
# analysis <- "microarray"
# imat <- buildKeggIncidence(kegg.ids, gene.ids, illuminaHumanv2.db,database, analysis, envPos) 
# ## End(Not run)