importCircMarker: Import circRNAs detected by CircMarker

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

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)

Aufiero/circRNAprofiler documentation built on Oct. 31, 2023, 1:18 a.m.