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

In nucleoSim: Generate synthetic nucleosome maps

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:

• call the matched call.

• dataIP a data.frame with the chromosome name, the starting and ending positions and the direction of all forward and reverse reads for all well-positioned and fuzzy nucleosomes.

• wp a data.frame with the positions of all the well-positioned nucleosomes, as well as the number of paired-reads associated to each one.

• fuz a data.frame with the positions of all the fuzzy nucleosomes, as well as the number of paired-reads associated to each one.

• paired a data.frame with the starting and ending positions of the reads used to generate the paired-end reads.

Author(s)

Astrid Deschenes

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)

nucleoSim documentation built on Nov. 8, 2020, 5:50 p.m.