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/" )
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 |
Creates a rda file for every chromosome defined in sel_chr
.
library(BSgenome.Hsapiens.UCSC.hg19)#>#>#>#> #>#>#> #>#>ref_gen <- BSgenome.Hsapiens.UCSC.hg19 hg19_dpnii <- digestGenome(res_enz="GATC", cut_pos=0, name_RE="dpnII", ref_gen=ref_gen, out_path="digested_genome/")#>#> #> #> #> #>#>