getBackSplicedJunctions: Import detected circRNAs

Description Usage Arguments Value See Also Examples

View source: R/getBackSplicedJunctions.R

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

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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

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check <- checkProjectFolder()

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

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

circRNAprofiler documentation built on Oct. 31, 2019, 3:23 a.m.