add_target_matches {multicrispr}R Documentation

Add target matches

Description

Add target matches

Usage

add_target_matches(
  spacers,
  targets,
  bsgenome,
  mismatches = 2,
  pam = "NGG",
  outdir = OUTDIR,
  verbose = TRUE
)

Arguments

spacers

GRanges

targets

GRanges

bsgenome

BSgenome

mismatches

number

pam

string

outdir

bowtie output directory

verbose

TRUE (default) or FALSE

Value

GRanges

Examples

require(magrittr)
file <- system.file('extdata/SRF.bed', package='multicrispr')
bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
targets0 <- bed_to_granges(file, 'mm10')
targets <- extend(targets0)
spacers <- find_spacers(targets, bsgenome, complement = FALSE, 
                        ontargetmethod = NULL, offtargetmethod = NULL)
spacers %<>% add_target_matches(targets, bsgenome)

[Package multicrispr version 1.4.0 Index]