annotateBSJs {circRNAprofiler} | R Documentation

## Annotate circRNA features.

### 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

    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

    # 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)

[Package circRNAprofiler version 1.8.0 Index]