plot_guide_fidelity

Show, for each position of the guide, the fidelity of the offtarget sequence as the percentage of matching bases.

Usage

plot_guide_fidelity(x, guide, pam)

Arguments

x

A GRanges object containing the results of a breakinspectoR analysis.

guide

character with the guide sequence. Only used for drawing, the number of mismatches is already present in `x`.

pam

character with PAM sequence. Only used for drawing, the number of mismatches is already present in `x`.

Value

Nothing.

Details

Currently this function has the limitation that does only *fixed* matching, expecting the offtarget sequence and the guide to show the same character. See ?`Biostrings::lowlevel-matching` for more information.

Examples

if (FALSE) { # \dontrun{
  offtargets <- breakinspectoR(
    target   =system.file("extdata/vegfa.chr6.bed.gz", package="breakinspectoR"),
    nontarget=system.file("extdata/nontarget.chr6.bed.gz", package="breakinspectoR"),
    guide    ="GACCCCCTCCACCCCGCCTC",
    PAM      =c("NGG", "NAG"),
    bsgenome ="BSgenome.Hsapiens.UCSC.hg38",
    cutsiteFromPAM=3
  )
} # }
data(breakinspectoR_examples)

plot_guide_fidelity(offtargets, guide="GACCCCCTCCACCCCGCCTC", pam="NGG")