getCircSeqs {circRNAprofiler} | R Documentation |
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.
getCircSeqs(annotatedBSJs, gtf, genome)
annotatedBSJs |
A data frame with the annotated back-spliced junctions.
It can be generated with |
gtf |
A data frame 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 <- getCircSeqs( annotatedBSJs, gtf, genome) }