gRNA: gRNA designer

In jianhong/CPD: CRISPR/Cas9 gRNA designer

Description

CRISPR/Cas9 gRNA designer.

Usage

gRNA(gr, upstream = 2000, downstream = 2000, anchor = c("TSS", "TES",
  "ALL", "onlyUpstream&Downstream"), species = c("mm10", "mm9", "hg19",
  "hg38", "danRer10"), ...)

Arguments

gr	A GRanges object or coordinates files could be converted into GRanges.
upstream, downstream	numeric(1).upstream or downstream of the coordinates.
anchor	Anchor point of upstream and downstream. TSS: search gRNAs for promoter of given coordinates.
species	character(1). Avaliable values: "mm9", "mm10", "hg19", "hg38", "danRer10"
...	Parameters could be passed to offTargetAnalysis. Default settings are: scoring.method = "CFDscore", annotatePaired = FALSE, max.mismatch=1

Value

invisible list of results of offTargetAnalysis

Examples

gr <- system.file('extdata', 'Sftpc.bed', package = 'CPD')
gRNA(gr, anchor="onlyUpstream&Downstream", species="mm10", 
       chromToSearch="chr14", outputDir="test")

jianhong/CPD documentation built on May 4, 2019, 8:40 a.m.