gdcExportNetwork: Export network for Cytoscape

In Jialab-UCR/GDCRNATools: GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

Description

Export nodes and edges of ce network for Cytoscape visualization

Usage

gdcExportNetwork(ceNetwork, net)

Arguments

ceNetwork	a dataframe generated from gdcCEAnalysis
net	one of 'nodes' and 'edges'

Value

A dataframe of nodes or edges

Author(s)

Ruidong Li and Han Qu

Examples

####### ceRNA network analysis #######
ceOutput <- data.frame(lncRNAs=c('ENSG00000242125','ENSG00000242125',
                                'ENSG00000245532'), 
                    Genes=c('ENSG00000043355','ENSG00000109586',
                                'ENSG00000144355'), 
                    miRNAs=c('hsa-miR-340-5p','hsa-miR-340-5p',
                            'hsa-miR-320b,hsa-miR-320d,
                            hsa-miR-320c,hsa-miR-320a'),
                    Counts=c(1,1,4), stringsAsFactors=FALSE)
####### Export edges #######
edges <- gdcExportNetwork(ceNetwork=ceOutput, net='edges')

####### Export nodes #######
## Not run: nodes <- gdcExportNetwork(ceNetwork=ceOutput, net='nodes')

Jialab-UCR/GDCRNATools documentation built on Nov. 28, 2020, 11:23 a.m.