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

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.

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

Nicola Licheri and Giulio Ferrero

Examples

if (FALSE) {

    #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")
}