circrnaClassification: Running CircHunter circRNA classification module

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

Running CircHunter circRNA classification module

Description

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.

Usage

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(s)

Nicola Licheri and Giulio Ferrero

Examples

## Not run: 

    #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")


## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.