getKcsmpAnn {SubpathwayMiner}R Documentation

Get the sub-pathways annotation and identification of metabolic network

Description

Annotate a set of genes to sub-pathways of metabolic pathways and identify the statistically significantly enriched sub-pathways.

Usage

getKcsmpAnn(geneList,background=getDefaultBackground(),k=4,
   order="pvalue",decreasing=FALSE)

Arguments

geneList A character vector of genes.
background A character vector of genes used to identify the statistically significantly enriched sub-pathways.
k An integer. A distance similarity parameter.
order A character string. Should be one of "pvalue", "qvalue".
decreasing A logical. Should the sort order be increasing or decreasing?

Details

The function can implement the sub-pathways annotation of metabolic pathways. It is the special form of the function getAnn where the argument graphList is the return value of the function getKcSubGraph. Detailed information is provided in getAnn.

Author(s)

Chunquan Li <lcqbio@yahoo.com.cn>

See Also

getMpAnn,getAnn, cutoffAnn,printAnn

Examples

##Annotate a set of genes to sub-pathways of metabolic pathways
 geneList<-getAexample(k=1000)
 ann<-getKcsmpAnn(geneList,k=4)
 printAnn(ann)[2:5]


[Package SubpathwayMiner version 2.0 Index]