Running CircHunter circRNA classification module

This function executes the docker container circhunter by running the circRNA classification module of CircHunter starting from a set of circRNAs. For CircHunter algorithm detail please refer to: https://github.com/carlo-deintinis/circhunter/tree/master/CircHunter.

circrnaClassification(
  group = c("sudo", "docker"),
  scratch.folder,
  circrna.data,
  exon.data,
  isoform.data,
  assembly = "hg19"
)

Arguments

group,

a character string. Two options: "sudo" or "docker", depending to which group the user belongs

scratch.folder,

a character string indicating the scratch folder where docker container will be mounted

circrna.data,

string indicating the path to the list of circRNAs

exon.data,

string indicating the path to the exon annotation file

isoform.data,

string indicating the path to the isoform annotation file

assembly,

string indicating the reference human genome assembly. Compatible assemblies: hg19 (default), hg18, hg38, mm9, mm10, rn6, dm6, ce11

Value

Two tab-delimited tables reporting the transcript- and gene-level classification of a list of circRNAs

Author

Nicola Licheri and Giulio Ferrero

Examples

if (FALSE) {

    #retrieve the example data
    system("wget https://github.com/carlo-deintinis/circhunter/archive/master.zip") #retrieve the example data
    system("unzip master.zip")

    #running the circrnaClassification function
    circrnaClassification(group="docker", scratch.folder="/data/scratch", circrna.data=paste(getwd(),"/circhunter-master/CircHunter/toyexample/toy_circRNA", sep=""), exon.data=paste(getwd(),"/circhunter-master/CircHunter/toyexample/toy_genome", sep=""), isoform.data=paste(getwd(),"/circhunter-master/CircHunter/toyexample/toy_isoformdata", sep=""), assembly="hg19")

}