SubpathwayMiner-internal {SubpathwayMiner}R Documentation

SubpathwayMiner internal functions

Description

These are functions internally called by other functions in the package SubpathwayMiner and not meant to be called by the user.

Usage

getAdjECID(ECID,top,direction)
getNodes(top)
getPathGraph(path,direction)
getAllPathGraph(fileList,path,direction,verbose=TRUE)
convertFile2List(file1,file2,sep="\t")
convertFile2List1(file1,file2,sep="\t")
getMerge(org="hsa",type1="enzyme",type2="ncbi-geneid",
    path="ftp://ftp.genome.jp/pub/kegg/genes/organisms")
getMerge1(org="hsa",type1="pathway",type2="ncbi-geneid",
    path="ftp://ftp.genome.jp/pub/kegg/genes/organisms")
buildBgGeneList(org="hsa",type2="ncbi-geneid",
    path="ftp://ftp.genome.jp/pub/kegg/genes/organisms")
initialize()
getKidFromOid(oid)
getOidFromKid(kid)
getkidoid(org,type2,path="ftp://ftp.genome.jp/pub/kegg/genes/organisms")
getPathName(file="map_title.tab",
    path="ftp://ftp.genome.jp/pub/kegg/pathway_gif")
isKOMPath(top)
getKOPathGraph(top)
getKONodes(top)
getAllKOPathGraph(fileList,path,verbose=TRUE)
getKOMPathGraph(top)
getAdjKOMID(KOID,top)

Author(s)

Chunquan Li <lcqbio@yahoo.com.cn>


[Package SubpathwayMiner version 2.0 Index]