Filters spacers which are specific for prime editing site

filter_prime_specific(
  spacers,
  bsgenome = getBSgenome(genome(spacers)[1]),
  pam = "NGG",
  outdir = OUTDIR,
  indexedgenomesdir = INDEXEDGENOMESDIR,
  verbose = TRUE
)

Arguments

spacers

spacer GRanges-class

bsgenome

BSgenome-class

pam

string (default 'NGG'): pam sequence

outdir

string: dir to which output is written

indexedgenomesdir

dir with bowtie-indexed genomes

verbose

TRUE (default) or FALSE

Value

filtered spacer GRanges-class

Examples

# PE example #----------- require(magrittr) bsgenome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38 gr <- char_to_granges(c(PRNP = 'chr20:4699600:+', # snp HBB = 'chr11:5227002:-', # snp HEXA = 'chr15:72346580-72346583:-', # del CFTR = 'chr7:117559593-117559595:+'), # ins bsgenome) spacers <- find_pe_spacers(gr, bsgenome)
# index_genome(bsgenome) # one time effort - takes few h # filter_prime_specific(spacers, bsgenome)