reduceOT — reduceOT • breakinspectoR

Does a very opinionated filtering of the OT detected by breakinspector.

Usage

reduceOT(
  x,
  fdr = 0.01,
  qval = 0.01,
  mismatches = 7,
  standard_chromosomes = TRUE,
  cores = getOption("mc.cores", 2L),
  verbose = TRUE
)

Arguments

x: A GRanges object containing the results of a breakinspectoR analysis.
fdr: numerical, keep only hits below this empirical FDR threshold.
qval: numerical, keep only hits below this q-value threshold.
mismatches: numeric, mismatches allowed between the guide and the genomic sequence.
standard_chromosomes: logical, constrain the analysis to standard chromosomes only (defaults to TRUE).
cores: numerical, number of parallel cores to use.
verbose: logical, keep informing about every step

Value

a GRanges object with the filtered OT.

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",
    eFDR     =FALSE,
    cutsiteFromPAM=3)
} # }
data(breakinspectoR_examples)

offtargets_filtered <- reduceOT(offtargets)
#> Keeping significant hits only (FDR<0.01 & qval<0.01)...FALSE
#>  done
#> Removing remove NNN* protospacers...
#>  done
#> Merging different OT in same protospacer...
#>  done
#> Merging same OT in different protospacers...
#>  done
#> Keeping standard chromosomes only...
#>  done