Filter for target-specific spacers

add_specificity(
  spacers,
  targets,
  bsgenome,
  mismatches = 2,
  pam = "NGG",
  outdir = OUTDIR,
  indexedgenomesdir = INDEXEDGENOMESDIR,
  plot = TRUE,
  verbose = TRUE
)

filter_target_specific(
  spacers,
  targets,
  bsgenome = getBSgenome(genome(spacers)[1]),
  mismatches = 2,
  pam = "NGG",
  outdir = OUTDIR,
  indexedgenomesdir = INDEXEDGENOMESDIR,
  plot = TRUE,
  verbose = TRUE
)

Arguments

spacers

spacer GRanges-class

targets

target GRanges-class

bsgenome

BSgenome-class

mismatches

number (default 2): max number of mismatches to consider

pam

string (default 'NGG'): pam sequence

outdir

directory where output is written to

indexedgenomesdir

string: dir with indexed genomes

plot

TRUE (default) or FALSE

verbose

TRUE (default) or FALSE

Value

filtered spacer GRanges-class

Examples

# TFBS example #------------- require(magrittr) bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 bedfile <- system.file('extdata/SRF.bed', package = 'multicrispr') targets <- extend(bed_to_granges(bedfile, genome = 'mm10'))
#> Read SRF.bed into GRanges
#> 1974 ranges on 21 chromosomes
spacers <- find_spacers(targets, bsgenome)
#> 3948 ranges after adding inverse strands
# index_genome(bsgenome) # spacers %<>% add_specificity(targets, bsgenome) # spacers %>% filter_target_specific(targets, bsgenome)