Basic4Cseq (version 1.8.0)

simulateDigestion: Simulate the digestion of a genome

Description

This function simulates the digestion process with two restriction enzymes for a dna sequence or a BSgenome package. The information can then be used for quality controls of the biological fragment library.

Usage

simulateDigestion(firstCutter, secondCutter, dnaSequence)

Arguments

firstCutter

First restriction enzyme sequence for the digestion process

secondCutter

Second restriction enzyme sequence for the digestion process

dnaSequence

DNA sequence that is digested

Value

Details

The resulting virtual library of fragment parts does not provide information on blind or non-blind fragments, but provides information on the fragment length distribution of the real (i.e. biological) 4C-seq library. In contrast to the regular virtual fragment library for 4C-seq data, fragments between two adjacent secondary restriction enzyme sites are counted as well.

Examples

  shortTestGenome = "ATCCATGTAGGCTAAGTACACATGTTAAGGTACAGTACAATTGCACGATCAT"
  fragments = simulateDigestion("catg", "gtac", shortTestGenome)
  head(fragments)