Find cas9 ranges in targetranges

find_cas9ranges(targetranges, verbose = TRUE)

Arguments

targetranges

GenomicRanges::GRanges

verbose

logical(1)

Value

GenomicRanges::GRanges

Examples

require(magrittr) bedfile <- system.file('extdata/SRF_sites.bed', package='multicrispr') bsgenome <- BSgenome.Mmusculus.UCSC.mm10::Mmusculus targetranges <- read_bed(bedfile, bsgenome) %>% flank_fourways()
#> Read C:/Users/abhagwa/Documents/multicrispr/inst/extdata/SRF_sites.bed
#> 1974 ranges on 21 chromosomes
#> 17 NT wide
#> 0 - 36535760 NT apart
#> Flank fourways
#> 1974 left flanks : [start-200, start-1]
#> 1974 right flanks : [end+1, end+200]
#> 3948 combined (left + right)
#> 7896 after adding strand-complements
#> 7306 after merging overlaps
find_cas9ranges(targetranges)
#> Find N{20}NGG cas9seqs
#> Rm 10 targetranges with no cas9sites
#> 9922 cas9 seqs across 33518 targetranges
#> GRanges object with 33518 ranges and 1 metadata column: #> seqnames ranges strand | seqs #> <Rle> <IRanges> <Rle> | <character> #> [1] chr1 4712436-4712458 + | CTCTAGAGTCACAGAACTTATGG #> [2] chr1 4712480-4712502 + | AATTTATTATGACTTACAGTCGG #> [3] chr1 4712524-4712546 + | TTCAGTTGCAGCTGTGAAAATGG #> [4] chr1 4712566-4712588 + | TTACTCAGTCTCACGCAAGCAGG #> [5] chr1 4712650-4712672 + | GAAGGTGTAGCCCAGATTAAAGG #> ... ... ... ... . ... #> [33514] chrY 89126327-89126349 - | AGCGTGGACACGCCCACCCTCGG #> [33515] chrY 89126684-89126706 - | CTTCCAGGCCCTAATAGCCGTGG #> [33516] chrY 89126655-89126677 - | TCTGGGCATAAGCTCCCCAATGG #> [33517] chrY 89126584-89126606 - | AAAGTCCAATCTCTCTGCTCTGG #> [33518] chrY 89126559-89126581 - | TCAAAGCAGCTGCATTTGCTCGG #> ------- #> seqinfo: 66 sequences (1 circular) from mm10 genome