getSeqsFromGRs {circRNAprofiler} | R Documentation

## Retrieve sequences flanking back-spliced junctions

### Description

The function getSeqsFromGRs() includes 3 modules to retrieve 3 types of sequences. Sequences of the introns flanking back-spliced junctions, sequences from a defined genomic window surrounding the back-spliced junctions and sequences of the back-spliced exons.

### Usage

    getSeqsFromGRs(annotatedBSJs, genome, lIntron = 100, lExon = 10, type = "ie")

### Arguments

`annotatedBSJs` | A data frame with the annotated back-spliced junctions. This data frame can be generated with `annotateBSJs`.
`genome` | A BSgenome object containing the genome sequences. It can be generated with in `getBSgenome`. See `available.genomes` to see the BSgenome package currently available
`lIntron` | An integer indicating how many nucleotides are taken from the introns flanking the back-spliced junctions. This number must be positive. Default value is 100.
`lExon` | An integer indicating how many nucleotides are taken from the back-spliced exons starting from the back-spliced junctions. This number must be positive. Default value is 10.
`type` | A character string specifying the sequences to retrieve. If type = "ie" the sequences are retrieved from the the genomic ranges defined by using the lIntron and lExon given in input. If type = "bse" the sequences of the back-spliced exons are retrieved. If type = "fi" the sequences of the introns flanking the back-spliced exons are retrieved. Default value is "ie".

### Value

A list.

### Examples

    # Load data frame containing predicted 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 <- getSeqsFromGRs(
        annotatedBSJs,
        genome,
        lIntron = 200,
        lExon = 10,
        type = "ie"
        )
    }

[Package circRNAprofiler version 1.8.0 Index]