circrnaPrepareFiles.Rd
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.
circrnaPrepareFiles( group = c("sudo", "docker"), scratch.folder, data.folder, assembly = "hg19", version = NULL )
group, | a character string. Two options: |
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scratch.folder, | a character string indicating the scratch folder where docker container will be mounted |
data.folder, | a character string indicating the data folder where the output files will be saved |
assembly, | string indicating the reference human genome assembly. Compatible assemblies: hg19 (default), hg18, hg38, mm9, mm10, rn6, dm6, ce11 |
version, | Ensembl database version used for the analysis. If no version number is provided, the last version is considered |
Two tab-delimited tables reporting the exons and the transcript isoforms annotations of an user-selected human genome assembly
if (FALSE) { #Download the example data system("wget https://github.com/carlo-deintinis/circhunter/archive/master.zip") system("unzip master.zip") #running the circrnaPrepareFiles function circrnaPrepareFiles(group="docker", scratch.folder="/data/scratch", data.folder="/data/output", assembly="hg19") }