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

Description Usage Arguments Details Value Author(s) References Examples

View source: R/findAttractorsStep.R

Description

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

Usage

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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

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## 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)

attract documentation built on Nov. 8, 2020, 8:04 p.m.