printAnn {SubpathwayMiner} | R Documentation |
Print the results of pathway annotation and identification.
printAnn(ann)
ann |
A list. The results returned from the function getAnn or getKOAnn . |
A data.frame of the annotation results. Its row names are pathway identifiers,
e.g, path:00010. Columns include (pathwayName, annGeneRatio, annBgRatio, pvalue, qvalue).
The annGeneRatio
is the ratio of the annotated genes ,e.g.,30/1000 means that
30 genes in 1000 genes are annotated.
The qvalue is the FDR-corrected q-value.
Chunquan Li <lcqbio@yahoo.com.cn>
##get an example of gene list geneList<-getAexample(k=1000) ##get annotation results ann<-getAnn(geneList) ##print results to screen printAnn(ann) ##print subset of columns to visilize well result<-printAnn(ann) result[,2:5] ##print subset of rows to visilize well result[1:10,] ##change print order of columns result[,c(4,3,2,5)] ##write the annotation results to tab delimited file. # Notices that the argument col.names=NA is essential. result<-printAnn(ann) write.table(result,file="result",col.names=NA,sep="\t")