Get [-3, +3] contextseqs for given cas9ranges

contextseqs(cas9ranges)

Arguments

cas9ranges

GenomicRanges::GRanges

Examples

require(magrittr) bedfile <- system.file('extdata/SRF_sites.bed', package = 'multicrispr') bsgenome <- BSgenome.Mmusculus.UCSC.mm10::Mmusculus cas9ranges <- read_bed(bedfile, bsgenome) %>% flank_fourways() %>% find_cas9ranges()
#> 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 N{20}NGG cas9seqs
#> Rm 10 targetranges with no cas9sites
#> 9922 cas9 seqs across 33518 targetranges
cas9ranges[1:3] %>% seqs()
#> [1] "CTCTAGAGTCACAGAACTTATGG" "AATTTATTATGACTTACAGTCGG" #> [3] "TTCAGTTGCAGCTGTGAAAATGG"
cas9ranges[1:3] %>% contextseqs()
#> [1] "GGTTCTCTAGAGTCACAGAACTTATGGACA" "AAGGAATTTATTATGACTTACAGTCGGCAG" #> [3] "ATTGTTCAGTTGCAGCTGTGAAAATGGAAG"