getBackSplicedJunctions {circRNAprofiler} | R Documentation

## Import detected circRNAs

### Description

The function getBackSplicedJunctions() reads the circRNAs_X.txt with the detected circRNAs, adapts the content and generates a unique data frame with all circRNAs identified by each circRNA detection tool and the occurrences found in each sample (named as reported in the column label in experiment.txt).

### Usage

    getBackSplicedJunctions(gtf, pathToExperiment = NULL)

### Arguments

`gtf` | A data frame containing the annotation information. It can be generated with `formatGTF`.
`pathToExperiment` | A string containing the path to the experiment.txt file. The file experiment.txt contains the experiment design information. It must have at least 3 columns with headers: label: (1st column) - unique names of the samples (short but informative). fileName: (2nd column) - name of the input files - e.g. circRNAs_X.txt, where x can be can be 001, 002 etc. group: (3rd column) - biological conditions - e.g. A or B; healthy or diseased if you have only 2 conditions. By default pathToExperiment is set to NULL and the file it is searched in the working directory. If experiment.txt is located in a different directory then the path needs to be specified.

### Value

A data frame.

### See Also

`backSplicedJunctions` for a description of the data frame containing back-spliced junctions coordinates.

### Examples

    check <- checkProjectFolder()

    if(check == 0){
    # Create gtf object
    gtf <- formatGTF(pathToGTF)

    # Read and adapt detected circRNAs
    backSplicedJunctions<- getBackSplicedJunctions(gtf)}

[Package circRNAprofiler version 1.1.0 Index]