circrnaMergePredictions.Rd
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") )
group, | a character string. Two options: |
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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. |
Two tab-delimited tables reporting the BS supporting reads and the coordinates of the filtered circRNAs are reported
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") }