add_genome_matches: Add genome matches

In multicrispr: Multi-locus multi-purpose Crispr/Cas design

Description

Add genome matches

Usage

add_genome_matches(
  spacers,
  bsgenome = getBSgenome(genome(spacers)[1]),
  mismatches = 2,
  pam = "NGG",
  offtargetmethod = c("bowtie", "pdict")[1],
  outdir = OUTDIR,
  indexedgenomesdir = INDEXEDGENOMESDIR,
  verbose = TRUE
)

Arguments

spacers	GRanges
bsgenome	BSgenome
mismatches	number
pam	string
offtargetmethod	'bowtie' or 'pdict'
outdir	bowtie output directory
indexedgenomesdir	directory with indexed genomes
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 %<>% extract(1:100)
spacers %<>% add_genome_matches(bsgenome)

multicrispr documentation built on Nov. 8, 2020, 5:10 p.m.