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

Description Usage Arguments Value Author(s) Examples

View source: R/nucleoSimInternFunctions.R

Description

Generate a synthetic nucleosome map using a synthetic nucleosome map.

Usage

1

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:

Author(s)

Astrid Deschenes

Examples

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## 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 May 6, 2019, 2:17 a.m.