add_genome_matches {multicrispr} | R Documentation |
Add genome matches
add_genome_matches( spacers, bsgenome = getBSgenome(genome(spacers)[1]), mismatches = 2, pam = "NGG", offtargetmethod = c("bowtie", "pdict")[1], outdir = OUTDIR, indexedgenomesdir = INDEXEDGENOMESDIR, verbose = TRUE )
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 |
GRanges
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)