getSeqsAcrossBSJs: Retrieve back-spliced junction sequences

Description Usage Arguments Value Examples

View source: R/getSeqsAcrossBSJs.R

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

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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

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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)

# 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)
}

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