getMpAnn {SubpathwayMiner} | R Documentation |
Annotate a set of genes to metabolic pathways.
getMpAnn(geneList,background=getDefaultBackground(), order="pvalue",decreasing=FALSE)
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? |
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
.
Chunquan Li <lcqbio@yahoo.com.cn>
getKcsmpAnn
,getAnn
, cutoffAnn
,printAnn
##annotate a set of genes to metabolic pathways geneList<-getAexample(k=1000) ann<-getMpAnn(geneList) printAnn(ann)