printAnn {SubpathwayMiner}R Documentation

Print the results of pathway annotation and identification

Description

Print the results of pathway annotation and identification.

Usage

     printAnn(ann)

Arguments

ann A list. The results returned from the function getAnn or getKOAnn.

Value

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.

Author(s)

Chunquan Li <lcqbio@yahoo.com.cn>

See Also

getAnn,getKOAnn,cutoffAnn

Examples

##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")

[Package SubpathwayMiner version 2.0 Index]