buildKeggIncidenceMatrix {attract} | R Documentation |
Internal function - buildings the KEGG incidence matrix requird by GSEAlm.
buildKeggIncidenceMatrix(kegg.ids, gene.ids, annotation, database, analysis, envPos, expressionSetGeneFormat)
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) |
This function is called internally by findAttractors
.
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.
Jessica Mar
Kanehisa, M. and S. Goto, KEGG: Kyoto Encyclopedia of Genes and Genomes. . Nucleic Acids Res., 2000. 28: p. 27-30.
## 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)