filtergRNAs {CRISPRseek} | R Documentation

## 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

### 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

[Package CRISPRseek version 1.32.0 Index]