getKcsmpAnn {SubpathwayMiner} | R Documentation |
Annotate a set of genes to sub-pathways of metabolic pathways and identify the statistically significantly enriched sub-pathways.
getKcsmpAnn(geneList,background=getDefaultBackground(),k=4, 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. |
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? |
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
.
Chunquan Li <lcqbio@yahoo.com.cn>
getMpAnn
,getAnn
, cutoffAnn
,printAnn
##Annotate a set of genes to sub-pathways of metabolic pathways geneList<-getAexample(k=1000) ann<-getKcsmpAnn(geneList,k=4) printAnn(ann)[2:5]