getBackSplicedJunctions: Import detected circRNAs

In Aufiero/circRNAprofiler: circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

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)}

Aufiero/circRNAprofiler documentation built on Nov. 3, 2024, 10:12 a.m.