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

Description Usage Arguments Value Author(s) Examples

View source: R/nucleoSimFunctions.R

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

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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:

Author(s)

Pascal Belleau, Rawane Samb, Astrid Deschenes

Examples

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## 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)

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