View source: R/getSeqsAcrossBSJs.R
getSeqsAcrossBSJs | R Documentation |
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.
getSeqsAcrossBSJs(annotatedBSJs, gtf, genome)
annotatedBSJs |
A data frame with the annotated back-spliced junctions.
It can be generated with |
gtf |
A dataframe containing genome annotation information. It can be
generated with |
genome |
A BSgenome object containing the genome sequences.
It can be generated with |
A list.
# 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)
}
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