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

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

Output restriction enzymes that recognize only the gRNA cleavage sites

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 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)

LihuaJulieZhu/CRISPRseek documentation built on Feb. 3, 2024, 2:44 p.m.