getSeqsAcrossBSJs {circRNAprofiler} | R Documentation

## Retrieve back-spliced junction sequences

### Description

The function getSeqsAcrossBSJs() retrieves the sequences across the back-spliced junctions. A total of 11 nucleotides from each side of the back-spliced junction are taken and concatenated together.

### Usage

    getSeqsAcrossBSJs(annotatedBSJs, gtf, genome)

### Arguments

`annotatedBSJs` | A data frame with the annotated back-spliced junctions. It can be generated with `annotateBSJs`.
`gtf` | A dataframe containing genome annotation information. It can be generated with `formatGTF`.
`genome` | A BSgenome object containing the genome sequences. It can be generated with `getBSgenome`. See `available.genomes` to see the BSgenome package currently available.

### Value

A list.

### 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)

    # Get genome
    if (requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)){

    genome <- BSgenome::getBSgenome("BSgenome.Hsapiens.UCSC.hg19")

    # Retrieve target sequences
    targets <- getSeqsAcrossBSJs(
        annotatedBSJs,
        gtf,
        genome)
    }

[Package circRNAprofiler version 1.6.0 Index]