add_offtargets.Rd
Add mcols 'off' (offtargets), 'off0' (0-mismatch offtargets), etc.
add_specificity(...) add_offtargets( spacers, bsgenome, targets = NULL, mismatches = 2, pam = "NGG", outdir = OUTDIR, indexedgenomesdir = INDEXEDGENOMESDIR, plot = TRUE, size_var = default_size_var(spacers), alpha_var = "off", verbose = TRUE )
... | to channel deprecated add_specificity to add_offtargets |
---|---|
spacers | spacer |
bsgenome | |
targets | NULL (default) or target
|
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 |
size_var | string: mapped to size in plot |
alpha_var | string: mapped to alpha in plot |
verbose | TRUE (default) or FALSE |
filtered spacer GRanges-class
For NULL targets: offtarget counts = (G0- 1) + G1 + ... Non-NULL targets: offtarget counts = (G0-T0) + (G1-T1) + ...
# 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_offtargets(spacers, bsgenome, mismatches=0) # add_offtargets(spacers, bsgenome, mismatches=2) # 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) # spacers %>% add_offtargets(bsgenome) # off = G - 1 # spacers %>% add_offtargets(bsgenome, targets) # off = G - T