Running circRNA reformat script

This function executes the docker container docker4circ to reformat circRNA prediction file produced by a certain tool in a common format to further analysis.

circrnaReformat(
  group = c("sudo", "docker"),
  scratch.folder,
  input.folder,
  output.folder,
  tool = c("acfs", "circexplorer", "circexplorer2", "circrnafinder", "ciri", "ciri2",
    "dcc", "findcirc2", "knife", "starchip", "uroborus")
)

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

input.folder,

string indicating the path of the folder which contains the input files to be reformatted

output.folder,

string indicating the path to the reformatted circRNA prediction files

tool,

string indicating the tool used to create the input files. Supported tools are: acfs, circexplorer, circexplorer2, circrnafinder, ciri, ciri2, dcc, findcirc2, knife, starchip, uroborus

Value

A circRNA list reformatted in a tab-delimited file storing the circRNA genomic coordinates

Author

Nicola Licheri

Examples

if (FALSE) {
}