Description Usage Arguments Value Author(s) Examples
Determines the sequence around a cut site using a fasta file or BSgenome
1 |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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")
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