filter_prime_specific.Rd
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 )
spacers | spacer |
---|---|
bsgenome | |
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 |
filtered spacer GRanges-class
# 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)