annotateBSJs: Annotate circRNA features.

Description Usage Arguments Value Examples

View source: R/annotateBSJs.R

Description

The function annotateBSJs() annotates the circRNA structure and the introns flanking the corresponding back-spliced junctions. The genomic features are extracted from the user provided gene annotation.

Usage

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annotateBSJs(
  backSplicedJunctions,
  gtf,
  isRandom = FALSE,
  pathToTranscripts = NULL
)

Arguments

backSplicedJunctions

A data frame containing the back-spliced junction coordinates (e.g. detected or randomly selected). For detected back-spliced junctions see getBackSplicedJunctions and mergeBSJunctions (to group circRNAs detected by multiple detection tools). For randomly selected back-spliced junctions see getRandomBSJunctions.

gtf

A data frame containing genome annotation information. It can be generated with formatGTF.

isRandom

A logical indicating whether the back-spliced junctions have been randomly generated with getRandomBSJunctions. Deafult value is FALSE.

pathToTranscripts

A string containing the path to the transcripts.txt file. The file transcripts.txt contains the transcript ids of the circRNA host gene to analyze. It must have one column with header id. By default pathToTranscripts is set to NULL and the file it is searched in the working directory. If transcripts.txt is located in a different directory then the path needs to be specified. If this file is empty or absent the longest transcript of the circRNA host gene containing the back-spliced junctions are considered in the annotation analysis.

Value

A data frame.

Examples

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# Load a data frame containing detected back-spliced junctions
data("mergedBSJunctions")

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

# Annotate the first back-spliced junctions
annotatedBSJs <- annotateBSJs(mergedBSJunctions[1, ], gtf)

Aufiero/circRNAprofiler documentation built on July 22, 2021, 9:34 p.m.