getCircSeqs: Retrieve circRNA sequences

Description Usage Arguments Value Examples

View source: R/getCircSeqs.R

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

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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

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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 <- getCircSeqs(
    annotatedBSJs,
    gtf,
    genome)

}

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