Generate a synthetic nucleosome map using a synthetic nucleosome map.
the length of each of the paired-end reads. Default = 40.
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.
the function call.
class "syntheticNucReads" containing the
call the matched call.
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.
data.frame with the positions of all the
well-positioned nucleosomes, as well as the number of paired-reads
associated to each one.
data.frame with the positions of all the fuzzy
nucleosomes, as well as the number of paired-reads associated to each one.
data.frame with the starting and ending
positions of the reads used to generate the paired-end reads.
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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)
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