find_spacers: Find crispr spacers in targetranges

In multicrispr: Multi-locus multi-purpose Crispr/Cas design

Description

Find crispr spacers in targetranges

Usage

find_spacers(
  gr,
  bsgenome,
  spacer = strrep("N", 20),
  pam = "NGG",
  complement = TRUE,
  ontargetmethod = c("Doench2014", "Doench2016")[1],
  offtargetmethod = c("bowtie", "pdict")[1],
  offtargetfilterby = character(0),
  subtract_targets = FALSE,
  mismatches = 2,
  indexedgenomesdir = INDEXEDGENOMESDIR,
  outdir = OUTDIR,
  verbose = TRUE,
  plot = TRUE,
  ...
)

Arguments

gr	GRanges-class
bsgenome	BSgenome-class
spacer	string: spacer pattern in extended IUPAC alphabet
pam	string: pam pattern in extended IUPAC alphabet
complement	TRUE (default) or FALSE: also search in compl ranges?
ontargetmethod	'Doench2016','Doench2016' or NULL (no on-target score)
offtargetmethod	'bowtie', 'pdict', or NULL (no offtarget analysis)
offtargetfilterby	filter for best off-target counts by this variable
subtract_targets	TRUE or FALSE (default): whether to subtract target (mis)matches from offtarget counts
mismatches	0-3: allowed mismatches in offtargetanalysis (choose mismatch=-1 to suppress offtarget analysis)
indexedgenomesdir	directory with Bowtie-indexed genomes (as produced with index_genome)
outdir	directory where bowtie analysis results are written to
verbose	TRUE (default) or FALSE
plot	TRUE (default) or FALSE
...	passed to plot_intervals

Value

GRanges-class

See Also

find_primespacers to find prime editing spacers

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)
    plot_intervals(gr)
    find_primespacers(gr, bsgenome)
    find_spacers(extend_for_pe(gr), bsgenome, complement=FALSE, mismatches=0)
          # complement = FALSE because extend_for_pe  already 
          # adds  reverse complements and does so in a strand-specific 
          # manner
    
# TFBS example
#-------------
    bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
    bedfile  <- system.file('extdata/SRF.bed', package='multicrispr')
    gr <- bed_to_granges(bedfile, 'mm10') %>% extend()
    gr %<>% extract(1:100)
    find_spacers(gr, bsgenome, subtract_targets = TRUE)

multicrispr documentation built on Nov. 8, 2020, 5:10 p.m.