importCircMarker {circRNAprofiler} | R Documentation

## Import circRNAs detected by CircMarker

### Description

The function importCircMarker is specifically designed to read and adapt the CircMarker (July.24.2018) output file (Brief_sum.txt). See https://github.com/lxwgcool/CircMarker for more details.

### Usage

    importCircMarker(pathToFile, gtf)

### Arguments

`pathToFile` | A character string specifying the path to the file containing the detected circRNAs.
`gtf` | A data frame containing the formatted GTF file. This is generated with `formatGTF`.

### Value

A data frame.

### Examples

    # Load short version of the gencode v19 annotation file
    data("gtf")

    # Path to an example file containing circRNA detected by CircMarker
    pathToFile <- system.file("extdata", "circmarker/circRNAs_001.txt",
        package="circRNAprofiler")

    # Inner function.
    # Import circRNAs.
    # Due to the short version of the gtf file gene names might miss in the
    # returned output.
    importCircMarker(pathToFile, gtf)

[Package circRNAprofiler version 1.4.2 Index]