filtergRNA: Filter gRNAs

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

Description

Filter gRNAs containing restriction enzyme cut site

Usage

filtergRNAs(all.gRNAs, pairOutputFile = "", 
    findgRNAsWithREcutOnly = FALSE,
    REpatternFile = system.file("extdata", "NEBenzymes.fa",
        package = "CRISPRseek"), format = "fasta", 
    minREpatternSize = 4, overlap.gRNA.positions = c(17, 18),overlap.allpos = TRUE)

Arguments

all.gRNAs	gRNAs as DNAStringSet, such as the output from findgRNAs
pairOutputFile	File path with paired gRNAs
findgRNAsWithREcutOnly	Indicate whether to find gRNAs overlap with restriction enzyme recognition pattern
REpatternFile	File path containing restriction enzyme cut patters
format	Format of the REpatternFile, default as fasta
minREpatternSize	Minimum restriction enzyme recognition pattern length required for the enzyme pattern to be searched for, default 4
overlap.gRNA.positions	The required overlap positions of gRNA and restriction enzyme cut site, default 17 and 18
overlap.allpos	Default TRUE, meaning that only gRNAs overlap with all the positions are retained FALSE, meaning that gRNAs overlap with one or both of the positions are retained

Value

gRNAs.withRE	gRNAs as DNAStringSet that passed the filter criteria
gRNAREcutDetails	a data frame that contains a set of gRNAs annotated with restriction enzyme cut details

Author(s)

Lihua Julie Zhu

See Also

offTargetAnalysis

Examples

    all.gRNAs <- findgRNAs(
        inputFilePath = system.file("extdata", "inputseq.fa", 
        package = "CRISPRseek"),
        pairOutputFile = "testpairedgRNAs.xls",
        findPairedgRNAOnly = TRUE)

    gRNAs.RE <- filtergRNAs(all.gRNAs = all.gRNAs,
        pairOutputFile = "testpairedgRNAs.xls",minREpatternSize = 6,
        REpatternFile = system.file("extdata", "NEBenzymes.fa", 
        package = "CRISPRseek"), overlap.allpos = TRUE)

    gRNAs  <- gRNAs.RE$gRNAs.withRE
    restriction.enzyme.cut.sites <- gRNAs.RE$gRNAREcutDetails

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