add_genome_matches {multicrispr}R Documentation

Add genome matches

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)

[Package multicrispr version 1.4.3 Index]