filter_target_specific.Rd
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 )
spacers | spacer |
---|---|
targets | target |
bsgenome | |
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 |
filtered spacer GRanges-class
# 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'))#>#>#># index_genome(bsgenome) # spacers %<>% add_specificity(targets, bsgenome) # spacers %>% filter_target_specific(targets, bsgenome)