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")
}