R Graphical Manual

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Last data update: 2014.03.03

R: Print the results of graph annotation and identification

printGraphW

R Documentation

Print the results of graph annotation and identification

Description

Print the results of graph annotation and identification.

Usage

     printGraphW(ann,detail=FALSE)

Arguments

`ann`	A list. The value was returned from the function `identifyLncGraphW`.
`detail`	A logical. If true, gene lists from the function `identifyLncGraphW` are converted into strings, which are used to display and write results with genes.

Value

A data.frame. Columns include pathwayId, pathwayName, annMoleculeRatio, annBgRatio,annWeight, pvalue, 'fdr', annMoleculeList, annBgMoleculeList. Detailed information is provided in identifyLncGraphW.

Author(s)

Xinrui Shi, Chunquan Li and Xia Li

Examples

## Not run: 
### Integrate lncRNAs of competitive regulation into KEGG pathway graphs ###
  LncGenePairs<-GetExampleData(exampleData="LncGenePairs")
  inteUMGraph<-getInteUMGraph(LncGenePairs)
### get user-interested lncRNAs and genes sets.
  geneLnc<-GetExampleData(exampleData="geneLnc")
# get locate subpathways.
  sub<-getLocSubGraphLnc(geneLnc,inteUMGraph,type="gene_lncRNA",n=1,s=8)
  SubcodeLncResult<-identifyLncGraphW(geneLnc,sub,type="gene_lncRNA",bet=1)
  resultT<-printGraphW(SubcodeLncResult,detail=TRUE)



## End(Not run)