Gene_Visualisation {IntramiRExploreR}R Documentation

Visualises the targetGene:miRNA network using Cytoscape and igraph .

Description

Visualises the targetGene:miRNA network using Cytoscape and igraph .

Usage

Gene_Visualisation(
  mRNA,
  mRNA_type = c("GeneSymbol", "FBGN", "CGID"),
  method = c("Pearson", "Distance", "Both"),
  platform = c("Affy1", "Affy2"),
  visualisation = c("igraph", "Cytoscape", "text", "console"),
  path = tempdir(),
  layout = c("kamadakawai", "reingold.tilford", "fruchterman.reingold", "interactive")
)

Arguments

mRNA

character. gene Identifier.

mRNA_type

character. mRNA id type. The choices are 'GeneSymbol','FBID' and 'CGID'.

method

character. Statistical Methods. Choices are 'Pearson','Distance','Both'

platform

character. Affymetrix Platforms. Choices are 'Affy1','Affy2'.

visualisation

character.Visualisation type. Choices are 'igraph','Cytoscape','text'and "console"

path

character. Path where data.frame is saved when visualisation is text. Default is tempdir().

layout

character. Network choices. Choices are 'kamadakawai','reingold.tilford','fruchterman.reingold' and 'interactive'.

Value

Depending upon the ouput choice network image or dataframe containg miRNAs that target the query gene are ouput.

Examples

mRNA='Syb'
Gene_Visualisation(mRNA,mRNA_type=c('GeneSymbol'),method=c('Pearson'),
                  platform=c('Affy1'), visualisation = "console")

[Package IntramiRExploreR version 1.15.2 Index]