cutoffAnn {SubpathwayMiner}R Documentation

Get the statistically significantly enriched pathways

Description

Get the statistically significantly enriched pathways according to the results returned from getAnn or getKOAnn function.

Usage

     cutoffAnn(ann,type="pvalue",operate="<=",cutoff=0.01)

Arguments

ann A list. The results returned from getAnn function.
type A character string. Should be one of "pvalue", "qvalue".
operate A character string. Should be one of "<","<=", ">", ">=".
cutoff A numeric. Detailed information is provided in getAnn.

Details

The function is used to identify the statistically signicantly enriched pathways compared with a background distribution. If users don't input background gene list in the function getAnn or getKOAnn, then background distribution will be obtained from the whole genome.

Value

A list of annotation results. Detailed information is provided in getAnn or getKOAnn.

Author(s)

Chunquan Li <lcqbio@yahoo.com.cn>

References

Strimmer,K. (2008). A unified approach to false discovery rate estimation.

See Also

getAnn,getKOAnn, printAnn

Examples

##get an example of gene sets
geneList<-getAexample(k=1000)

##get the annotated results
 ann<-getAnn(geneList)

##get the statistically signicantly enriched pathways according to pvalue<0.001
 cutedAnn<-cutoffAnn(ann,"pvalue","<",0.001)

##print results to screen
 printAnn(cutedAnn)


[Package SubpathwayMiner version 2.0 Index]