circrnaReformat: Running circRNA reformat script

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

Running circRNA reformat script

Description

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

Usage

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(s)

Nicola Licheri

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