getSeqsFromGRs: Retrieve sequences flanking back-spliced junctions

In circRNAprofiler: circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

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"
    )
}

circRNAprofiler documentation built on March 6, 2021, 2 a.m.