cutoffAnn {SubpathwayMiner} | R Documentation |
Get the statistically significantly enriched pathways
according to the results returned from getAnn
or getKOAnn
function.
cutoffAnn(ann,type="pvalue",operate="<=",cutoff=0.01)
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 . |
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.
A list of annotation results. Detailed information is provided in getAnn
or getKOAnn
.
Chunquan Li <lcqbio@yahoo.com.cn>
Strimmer,K. (2008). A unified approach to false discovery rate estimation.
##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)