CRISPRseek (version 1.12.0)

filtergRNAs: Filter gRNAs

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

Details

References

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