getMpAnn {SubpathwayMiner}R Documentation

get annotation informations of metabolic pathways

Description

Annotate a set of genes to metabolic pathways based on EC.

Usage

  getMpAnn(geneList,background=getDefaultBackground(),
   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.
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 annotation and identification of metabolic pathways. It is the special form of the function getAnn where the argument graphList is the return value of the function getDefaultUndirectedGraph. Detailed information is provided in getAnn.

Author(s)

Chunquan Li <lcqbio@yahoo.com.cn>

See Also

getKcsmpAnn,getAnn, cutoffAnn,printAnn

Examples

##annotate a set of genes to metabolic pathways
 geneList<-getAexample(k=1000)
 ann<-getMpAnn(geneList)
 printAnn(ann)


[Package SubpathwayMiner version 2.0 Index]