Description Usage Arguments Value Author(s) Examples
View source: R/nucleoSimFunctions.R
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).
1 | syntheticNucReadsFromMap(syntheticNucMap, read.len = 40, offset)
|
syntheticNucMap |
a |
read.len |
a positive |
offset |
a non-negatvie |
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.
Pascal Belleau, Rawane Samb, Astrid Deschenes
1 2 3 4 5 6 7 8 9 10 11 | ## 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)
|
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