uniqueREs: Output restriction enzymes that recognize only the gRNA...

In CRISPRseek: Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

Description

For each identified gRNA, output restriction enzymes that recognize only the gRNA cleavage sites.

Usage

uniqueREs(REcutDetails, summary, offTargets, scanUpstream = 100,
   scanDownstream = 100, BSgenomeName)

Arguments

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

Value

returns the RE sites that recognize only the gRNA cleavage sites for each gRNA.

Author(s)

Lihua Julie Zhu

Examples

    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)

CRISPRseek documentation built on Jan. 14, 2021, 2:50 a.m.