circrnaMergePredictions: Function to merge different circRNA lists predicted from one...

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

Function to merge different circRNA lists predicted from one of the supported circRNA prediction tools.

Description

This function executes the docker container ciri2merge by running the merge of different lists of circRNAs predicted by one of the supported tools following a sample data files provided by the user. The function executes also a filter based on the number of back-splicing reads computed in each experiment and across replicates of the same biological condition.

Usage

circrnaMergePredictions(
  group = c("sudo", "docker"),
  scratch.folder,
  data.folder,
  samples.list,
  covariates.list,
  covariate.order,
  min_reads = 2,
  min_reps = 0,
  min_avg = 10,
  used.tool = c("acfs", "ciri", "ciri2", "circexplorer", "circexplorer2",
    "circrnafinder", "dcc", "findcirc2", "knife")
)

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
data.folder	a character string indicating the data folder where the circRNA output files are located
samples.list	a character vector indicating the identifiers of the samples
covariates.list	a character vector indicating the classes of the samples
covariate.order	a character vector indicating the order of covariates in the output files
min_reads	the minimum number of back-splicing reads supporting a circRNA and detected in at least min_reps number of biological replicates of the same experimental condition (default = 2)
min_reps	the minimum number of replicates associated with at least min_reads supporting a circRNA (default = 0)
min_avg	the average number of back-splicing reads across biological replicates of the same experimental condition that shall support a circRNA (default = 10)
used.tool	the tool used to predict the circRNAs. Supported tools are: ACFS, CIRI, CIRI2, CIRCexplorer, CIRCexplorer2, CircRNA_Finder, DCC, Find_Circ2, KNIFE, Uroborus.

Value

Two tab-delimited tables reporting the BS supporting reads and the coordinates of the filtered circRNAs are reported

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")
    system("unzip ./circhunter-master/CircHunter/data/CIRI_predictions.zip")

    #running the circrnaMergePredictions function
    circrnaMergePredictions(group="docker", scratch.folder="/data/scratch", data.folder="./circhunter-master/CircHunter/data/CIRI_predictions", groups.file="./circhunter-master/CircHunter/data/CIRI_predictions/SampleData.tsv", min_reads = 2, min_reps = 2, min_avg = 10, used.tool="ciri2")

## End(Not run)

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