mergeMotifs {circRNAprofiler} | R Documentation |
A same RBP can recognize multiple motifs, the function mergeMotifs() groups all the motifs found for each RBP and report the total counts.
mergeMotifs(motifs)
motifs |
A data frame generated with |
A data frame.
# Load data frame containing detected back-spliced junctions data("mergedBSJunctions") # Load short version of the gencode v19 annotation file data("gtf") # Example with the first back-spliced junctions. # Multiple back-spliced junctions can also be analyzed at the same time. # Annotate detected back-spliced junctions annotatedBSJs <- annotateBSJs(mergedBSJunctions[1, ], gtf) # Get genome genome <- BSgenome::getBSgenome("BSgenome.Hsapiens.UCSC.hg19") # Retrieve target sequences targets <- getSeqsFromGRs( annotatedBSJs, genome, lIntron = 200, lExon = 10, type = "ie" ) # Get motifs motifs <- getMotifs( targets, width = 6, species = "Hsapiens", rbp = TRUE, reverse = FALSE) # Group motifs mergedMotifs <- mergeMotifs(motifs)