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
)

Arguments

spacers

spacer GRanges-class

bsgenome

BSgenome-class

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

Value

spacer GRanges with additional mcols

Details

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.

See also

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) # 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'))
#> Read SRF.bed into GRanges
#> 1974 ranges on 21 chromosomes
spacers <- find_spacers(targets, bsgenome)
#> 3948 ranges after adding inverse strands
# index_genome(bsgenome) # add_genome_counts(spacers, bsgenome) # add_genome_counts(spacers, bsgenome, mismatches=3)