add_genome_counts.Rd
Count spacer matches to genome and add to GRanges
add_genome_counts( spacers, bsgenome = getBSgenome(genome(spacers)[1]), mismatches = 2, pam = "NGG", outdir = OUTDIR, indexedgenomesdir = INDEXEDGENOMESDIR, plot = FALSE, verbose = TRUE )
spacers | spacer |
---|---|
bsgenome | |
mismatches | number (default 2): max number of mismatches to consider |
pam | string (default 'NGG') pam pattern to expand |
outdir | dir where output is written to |
indexedgenomesdir | string: dir with indexed genomes |
plot | FALSE (default) or TRUE |
verbose | TRUE (default) or FALSE |
spacer GRanges with additional mcols
Expands iupac amgiguities in the pam sequence. Matches all resulting sequences against (indexes) target and genome. Adds match counts to GRanges object, and then returns it.
# 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) # add_genome_counts(spacers, bsgenome, mismatches=0, plot = TRUE) # TFBS example #------------- 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) # add_genome_counts(spacers, bsgenome) # add_genome_counts(spacers, bsgenome, mismatches=3)