CRISPRseek (version 1.12.0)

searchHits: Search for off targets

Description

Search for off targets for given gRNAs, BSgenome and maximum mismatches

Usage

searchHits(gRNAs, BSgenomeName, chromToSearch = "all", chromToExclude = "", max.mismatch = 3,  PAM.size = 3, gRNA.size = 20, PAM = "N[A|G]G$", allowed.mismatch.PAM = 2)

Arguments

gRNAs

DNAStringSet object containing a set of gRNAs. Please note the sequences must contain PAM appended after gRNAs, e.g., ATCGAAATTCGAGCCAATCCCGG where ATCGAAATTCGAGCCAATCC is the gRNA and CGG is the PAM

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, and BSgenome.Dmelanogaster.UCSC.dm3 for dm3

chromToSearch

Specify the chromosome to search, default to all, meaning search all chromosomes. For example, chrX indicates searching for matching in chromosome X only

chromToExclude

Specify the chromosome not to search, default to none, meaning to search chromosomes specified by chromToSearch. For example, to exclude haplotype blocks from offtarget search in hg19, set chromToExclude to c(""chr17_ctg5_hap1","chr4_ctg9_hap1", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3", "chr6_mann_hap4", "chr6_mcf_hap5","chr6_qbl_hap6", "chr6_ssto_hap7")

max.mismatch

Maximum mismatch allowed in off target search, default 3. Warning: will be considerably slower if it is set to greater than 3

PAM.size

Size of PAM, default 3

gRNA.size

Size of gRNA, default 20

PAM

Regular expression of PAM, default N[A|G]G$

allowed.mismatch.PAM

Number of degenerative bases in the PAM sequence, default to 2 for N[A|G]G PAM

Value

a data frame contains IsMismatch.posX (indicator variable indicating whether this position X is mismatch or not, 1 means yes and 0 means not, X = 1 to gRNA.size) representing all positions in the gRNA),strand (strand of the match, + for plus and - for minus strand), chrom (chromosome of the off target), chromStart (start position of the off target), chromEnd (end position of the off target),name (gRNA name), gRNAPlusPAM (gRNA sequence with PAM sequence concatenated), OffTargetSequence (the genomic sequence of the off target), n.mismatch (number of mismatches between the off target and the gRNA), forViewInUCSC (string for viewing in UCSC genome browser, e.g., chr14:31665685-31665707), score (set to 100, and will be updated in getOfftargetScore)

Details

References

See Also

offTargetAnalysis

Examples

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

    library("BSgenome.Hsapiens.UCSC.hg19")
    ### for speed reason, use max.mismatch = 0 for finding all targets with 
    ### all variants of PAM
    hits <- searchHits(all.gRNAs[1], BSgenomeName = Hsapiens,
        max.mismatch = 0, chromToSearch = "chrX")
    colnames(hits)