View source: R/nucleoSimInternFunctions.R
createNucReadsFromNucMap | R Documentation |
Generate a synthetic nucleosome map using a synthetic nucleosome map.
createNucReadsFromNucMap(map, read.len, offset, call)
map |
a |
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. |
an 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.
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.
Astrid Deschenes
## 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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