checkCuts {msgbsR} | R Documentation |
Determines the sequence around a cut site using a fasta file or BSgenome
checkCuts(cutSites, genome, fasta = FALSE, seq)
cutSites |
A GRanges object containing the locations of the cut sites to be checked for sequence match. The names of the correct cut sites will be returned as a GRanges object. |
genome |
The path to a fasta file or a BSgenome object to check for genomic sequences. |
fasta |
TRUE if a fasta file has been supplied. Default = FALSE |
seq |
The desired recognition sequence that the enzyme should have cut. |
A GRanges object containing the names of the sites that had the correct sequence.
Benjamin Mayne
library(GenomicRanges) library(SummarizedExperiment) library(BSgenome.Rnorvegicus.UCSC.rn6) # Load the positions of possible MspI cut sites data(ratdata) # Extract the cut sites cutSites <- rowRanges(ratdata) # Adjust the cut sites to overlap recognition site on each strand start(cutSites) <- ifelse(test = strand(cutSites) == '+', yes = start(cutSites) - 1, no = start(cutSites) - 2) end(cutSites) <- ifelse(test = strand(cutSites) == '+', yes = end(cutSites) + 2, no = end(cutSites) + 1) correctCuts <- checkCuts(cutSites = cutSites, genome = "rn6", seq = "CCGG")