nucleoSim (version 1.0.2)

createNucReadsFromNucMap: Create a synthetic nucleosome reads from a synthetic nucleosome map

Description

Generate a synthetic nucleosome map using a synthetic nucleosome map.

Usage

createNucReadsFromNucMap(map, read.len, offset, call)

Arguments

map

a list of class "syntheticNucMap"

read.len

the length of each of the paired-end reads. Default = 40.

offset

the number of bases used to offset all nucleosomes and reads. This is done to ensure that all nucleosome positions and read alignment are of positive values.

call

the function call.

Value

• an list of class "syntheticNucReads" containing the following elements:
  • callthe matched call.
  • dataIPadata.framewith the chromosome name, the starting and ending positions and the direction of all forward and reverse reads for all well-positioned and fuzzy nucleosomes.
  • wpadata.framewith the positions of all the well-positioned nucleosomes, as well as the number of paired-reads associated to each one.
  • fuzadata.framewith the positions of all the fuzzy nucleosomes, as well as the number of paired-reads associated to each one.
  • pairedadata.framewith the starting and ending positions of the reads used to generate the paired-end reads.

Examples

## Generate a synthetic map with 30 well-positioned nucleosomes, 5 fuzzy
## nucleosomes and 6 deleted nucleosomes using a Student distribution
## with a variance of 10 for the well-positioned nucleosomes,
## a variance of 15 for the fuzzy nucleosomes and a seed of 1335
map_call <- call("syntheticNucMapFromDist", wp.num = 30, wp.del = 6,
wp.var = 10, fuz.num = 5, fuz.var = 15, rnd.seed = 1335,
distr = "Student")
syntheticMap <- eval(map_call)

syntheticReads <- nucleoSim:::createNucReadsFromNucMap(syntheticMap,
read.len = 40, offset = 1000, call = map_call)