CRISPRseek (version 1.12.0)

writeHits: Write the hits of sequence search to a file

Description

write the hits of sequence search to a file, internal function used by searchHits

Usage

writeHits(gRNA, seqname, matches, strand, file, gRNA.size = 20,  PAM = "N[A|G]G$", max.mismatch = 4, chrom.len, append = FALSE)

Arguments

gRNA

DNAString object with gRNA sequence with PAM appended immediately after,e.g., ACGTACGTACGTACTGACGTCGG with 20bp gRNA sequence plus 3bp PAM sequence CGG

seqname

chromosome name as character, e.g., chr1

matches

XStringViews object storing matched chromosome locations

strand

strand of the match, + for plus strand and - for minus strand

file

file path where the hits is written to

gRNA.size

gRNA size, default 20

PAM

PAM as regular expression for filtering the hits, default N[A|G]G$

max.mismatch

maximum mismatch allowed within the gRNA (excluding PAM portion) for filtering the hits, default 4

chrom.len

length of the matched chromosome

append

TRUE if append to existing file, false if start a new file

Value

results are saved in the file specified by file

Details

References

http://bioconductor.org/packages/2.8/bioc/vignettes/BSgenome/inst/doc/ GenomeSearching.pdf

See Also

offTargetAnalysis

Examples

    gRNAPlusPAM <- DNAString("ACGTACGTACGTACTGACGTCGG")
    x <- DNAString("AAGCGCGATATGACGTACGTACGTACTGACGTCGG")
    chrom.len <- nchar(as.character(x))
    m <- matchPattern(gRNAPlusPAM, x)
    names(m) <- "testing"
    writeHits(gRNA = gRNAPlusPAM, seqname = "chr1", 
        matches = m, strand = "+", file = "exampleWriteHits.txt", 
        chrom.len = chrom.len, append = FALSE)