writeHits: Write the hits of sequence search from a sequence to a file

writeHitsR Documentation

Write the hits of sequence search from a sequence to a file

Description

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

Usage

writeHits(
  gRNA,
  seqname,
  matches,
  strand,
  file,
  gRNA.size = 20L,
  PAM = "NGG",
  PAM.pattern = "N[A|G]G$",
  max.mismatch = 4L,
  chrom.len,
  append = FALSE,
  PAM.location = "3prime",
  PAM.size = 3L,
  allowed.mismatch.PAM = 1L,
  seqs,
  baseEditing = FALSE,
  targetBase = "C",
  editingWindow = 4:8
)

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

sequence name as character

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 appending to the gRNA, default NGG for SpCas9, change to TTTN for cpf1.

PAM.pattern

PAM as regular expression for filtering the hits, default N[A|G]G$ for spCas9. For cpf1, ^TTTN since it is a 5 prime PAM sequence.

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

PAM.location

PAM location relative to gRNA. For example, spCas9 PAM is located on the 3 prime while cpf1 PAM is located on the 5 prime

PAM.size

Size of PAM, default 3

allowed.mismatch.PAM

Maximum number of mismatches allowed in the offtargets comparing to the PAM sequence. Default to 1 for NGG PAM

seqs

DNAString object containing a DNA sequence.

baseEditing

Indicate whether to design gRNAs for base editing. Default to FALSE If TRUE, please set baseEditing = TRUE, targetBase and editingWidow accordingly.

targetBase

Applicable only when baseEditing is set to TRUE. It is used to indicate the target base for base editing systems, default to C for converting C to T in the CBE system. Please change it to A if you intend to use the ABE system.

editingWindow

Applicable only when baseEditing is set to TRUE. It is used to indicate the effective editing window to consider for the offtargets search only, default to 4 to 8 which is for the original CBE system. Please change it accordingly if the system you use have a different editing window, or you would like to include offtargets with the target base in a larger editing window.

Value

results are saved in the file specified by file

Author(s)

Lihua Julie Zhu

References

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

See Also

offTargetAnalysis

Examples


 if(interactive())
 {
    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, seqs = x)
 }

LihuaJulieZhu/CRISPRseek documentation built on Feb. 3, 2024, 2:44 p.m.