uniqueREs {CRISPRseek} | R Documentation |
For each identified gRNA, output restriction enzymes that recognize only the gRNA cleavage sites.
uniqueREs(REcutDetails, summary, offTargets, scanUpstream = 100, scanDownstream = 100, BSgenomeName)
REcutDetails |
REcutDetails stored in the REcutDetails.xls |
summary |
summary stored in the summary.xls |
offTargets |
offTargets stored in the offTargets.xls |
scanUpstream |
upstream offset from the gRNA start, default 100 |
scanDownstream |
downstream offset from the gRNA end, default 100 |
BSgenomeName |
BSgenome object. Please refer to available.genomes in BSgenome package. For example, BSgenome.Hsapiens.UCSC.hg19 for hg19, BSgenome.Mmusculus.UCSC.mm10 for mm10, BSgenome.Celegans.UCSC.ce6 for ce6, BSgenome.Rnorvegicus.UCSC.rn5 for rn5, BSgenome.Drerio.UCSC.danRer7 for Zv9, and BSgenome.Dmelanogaster.UCSC.dm3 for dm3 |
returns the RE sites that recognize only the gRNA cleavage sites for each gRNA.
Lihua Julie Zhu
library("BSgenome.Hsapiens.UCSC.hg19") load(system.file("extdata", "ForTestinguniqueREs.RData", package = "CRISPRseek")) uniqueREs(results$REcutDetails, results$summary, results$offtarget, scanUpstream = 50, scanDownstream = 50, BSgenomeName = Hsapiens)