Digest reference genome

Performs an in silico digestion of a given reference genome using a given restriction enzyme sequence.

digestGenome(
  res_enz,
  cut_pos,
  name_RE,
  ref_gen,
  sel_chr = paste0("chr", c(seq_len(22), "X", "Y")),
  out_path = "digested_genome/"
)

Arguments

res_enz	Character containing the restriction enzyme sequence.
cut_pos	Numeric indicating the nucleotide position where restriction enzyme cuts (zero-based) (for example, for DpnII is 0).
name_RE	Restriction enzyme name.
ref_gen	A BSgenome object of the reference genome.
sel_chr	Character vector indicating which chromosomes to select for the digestion. Default: chr1-22, chrX, chrY.
out_path	Output path where to save the genomic track. The default is a directory named digested_genome/ created in your working directory. The rda objects are saved in folder named by the ref_gene_name_RE in the out_path folder.

Value

Creates a rda file for every chromosome defined in sel_chr.

Examples

library(BSgenome.Hsapiens.UCSC.hg19)
#> Loading required package: BSgenome
#> Loading required package: Biostrings
#> Loading required package: XVector
#> 
#> Attaching package: ‘Biostrings’
#> The following object is masked from ‘package:base’:
#> 
#>     strsplit
#> Loading required package: rtracklayer
ref_gen <- BSgenome.Hsapiens.UCSC.hg19

hg19_dpnii <- digestGenome(
    res_enz = "GATC",
    cut_pos = 0,
    name_RE = "dpnII",
    sel_chr = "chr16", # Only in chr16 to reduce example running time
    ref_gen = ref_gen,
    out_path = file.path(tempdir(), "digested_genome/")
)
#> Generating digested genome using:
#>  > Restriction enzyme sequence: GATC 
#>  > Restriction enzyme cut position: 0 
#>  > Restriction enzyme name: dpnII 
#>  > Reference genome: BSgenome.Hsapiens.UCSC.hg19 
#>  > Output path: /tmp/RtmpLHTq6n/digested_genome/
#> Finished genome digestion.