syntheticNucReadsFromMap: Generate a synthetic nucleosome map containing forward and...

In ArnaudDroitLab/nucleoSim: Generate synthetic nucleosome maps

Generate a synthetic nucleosome map containing forward and reverse reads

Description

Generate a synthetic nucleosome map using a synthetic nucleosome map.

This function is using a modified version of the syntheticNucMap() function from Bioconductor nucleR package (Flores and Orozco, 2011).

Usage

syntheticNucReadsFromMap(syntheticNucMap, read.len = 40, offset)

Arguments

syntheticNucMap	a list of class "syntheticNucMap"
read.len	a positive integer, the length of each of the paired-end reads. Default = 40.
offset	a non-negatvie integer,the number of bases used to offset all nucleosomes and reads. This is done to ensure that all nucleosome positions and read alignments are of positive values.

Value

a 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. Paired-end reads are identified with an unique id.

• 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. Paired-end reads are identified with an unique id.

Author(s)

Pascal Belleau, Rawane Samb, Astrid Deschenes

Examples

## Generate a synthetic map with 20 well-positioned + 10 fuzzy nucleosomes
## using a Normal distribution with a variance of 30 for the well-positioned
## nucleosomes, a variance of 40 for the fuzzy nucleosomes and a seed of 15
## Because of the fixed seed, each time is going to be run, the results
## are going to be the seed
syntheticMap <- syntheticNucMapFromDist(wp.num = 20, wp.del = 0,
    wp.var = 30, fuz.num = 10, fuz.var = 40,
    rnd.seed = 335, as.ratio = FALSE, distr = "Uniform")

res <- nucleoSim:::syntheticNucReadsFromMap(syntheticMap, read.len = 45,
    offset = 1000)

ArnaudDroitLab/nucleoSim documentation built on March 17, 2022, 11 p.m.