importCircMarker: Import circRNAs detected by CircMarker

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

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)

circRNAprofiler documentation built on March 6, 2021, 2 a.m.