buildKeggIncidenceMatrix {attract} | R Documentation

## 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, 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)

[Package attract version 1.42.0 Index]