getCircSeqs: Retrieve circRNA sequences

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

Retrieve circRNA sequences

Description

The function getCircSeqs() retrieves the circRNA sequences. The circRNA sequence is given by the sequences of the exons in between the back-spliced-junctions.The exon sequences are retrieved and then concatenated together to recreate the circRNA sequence. To recreate the back-spliced junction sequence 50 nucleotides are taken from the 5' head and attached at the 3' tail of each circRNA sequence.

Usage

getCircSeqs(annotatedBSJs, gtf, genome)

Arguments

annotatedBSJs	A data frame with the annotated back-spliced junctions. It can be generated with annotateBSJs.
gtf	A data frame 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 <- getCircSeqs(
    annotatedBSJs,
    gtf,
    genome)

}

Aufiero/circRNAprofiler documentation built on Oct. 31, 2023, 1:18 a.m.