buildKeggIncidenceMatrix: Internal function - buildings the KEGG incidence matrix...

In jmarlab/attract: Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

Description

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

Usage

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

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.
expressionSetGeneFormat	a character string specifying the type of identifier for a gene in your expression data set. The default value is NULL. (ex. SYMBOL, ENTREZID, REFSEQ, ENSEMBL)

Details

This function is called internally by findAttractors.

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.

Author(s)

Jessica Mar

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)

jmarlab/attract documentation built on May 23, 2019, 9:02 p.m.