circrnaAnnotations: Annotation of a list of circRNAs

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

Annotation of a list of circRNAs

Description

This function executes the docker container ciri2 in the annotation mode to overlap a list of circRNAs with the annotations from circBase, CSCD, ExoRBase, Circ2Disease, CircFunBase, and TSCD

Usage

circrnaAnnotations(
  group = c("sudo", "docker"),
  scratch.folder,
  ciri.file,
  annotation.sources = c("circbase", "tscd", "cscd", "exorbase", "circ2disease",
    "circfunbase"),
  assembly = c("hg18", "hg19", "hg38", "mm9", "mm10")
)

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
ciri.file	a list of circRNAs derived from a circRNAs prediction analysis
annotation.sources	a vector of character strings indicating the circRNA databases to analyse. Compatible databases id: circbase, cscd, exorbase, circ2disease, circfunbase, tscd.
assembly	a character string indicating the reference genome assembly. The function currently work with the hg18, hg19, and hg38, mm9, and mm10 genome assemblies.

Value

The annotations of a list of circRNAs from different databases

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")
    system("unzip master.zip")

# Run the circAnnotations function
 circAnnotations(group = "docker", scratch.folder="/data/scratch", ciri.file=paste(getwd(),"/circhunter-master/CircHunter/data/circRNA_CRC.bed", sep=""), assembly="hg19")

circAnnotations()

## End(Not run)

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