getSeqsFromGRs {circRNAprofiler} | R Documentation |
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.
getSeqsFromGRs(annotatedBSJs, genome, lIntron = 100, lExon = 10, type = "ie")
annotatedBSJs |
A data frame with the annotated back-spliced junctions.
This data frame can be generated with |
genome |
A BSgenome object containing the genome sequences.
It can be generated with in |
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". |
A list.
# 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" ) }