Get BSgenome

get_bsgenome(granges)

Arguments

granges

GenomicRanges::GRanges

Value

BSgenome

Examples

require(magrittr) bedfile <- system.file('extdata/SRF_sites.bed', package='multicrispr') bsgenome <- BSgenome.Mmusculus.UCSC.mm10::Mmusculus granges <- 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
granges %>% get_bsgenome()
#> Mouse genome: #> # organism: Mus musculus (Mouse) #> # provider: UCSC #> # provider version: mm10 #> # release date: Dec. 2011 #> # release name: Genome Reference Consortium GRCm38 #> # 66 sequences: #> # chr1 chr2 chr3 #> # chr4 chr5 chr6 #> # chr7 chr8 chr9 #> # chr10 chr11 chr12 #> # chr13 chr14 chr15 #> # ... ... ... #> # chrUn_GL456372 chrUn_GL456378 chrUn_GL456379 #> # chrUn_GL456381 chrUn_GL456382 chrUn_GL456383 #> # chrUn_GL456385 chrUn_GL456387 chrUn_GL456389 #> # chrUn_GL456390 chrUn_GL456392 chrUn_GL456393 #> # chrUn_GL456394 chrUn_GL456396 chrUn_JH584304 #> # (use 'seqnames()' to see all the sequence names, use the '$' or '[[' operator #> # to access a given sequence)