runCHR {RJMCMCNucleosomes} | R Documentation |
rjmcmc
on multiples segments and merge results.Run rjmcmc
on a segment that is contained
in a list
of segments. Files generated by the function are all saved
in a directory specified by user. A RData log file is created when a
segment has been run while the result is saved in a RDS file.
If the same output directory is used more than once, the
rjmcmc
won't be called for segments that have the à
corresponding RData log file.
runCHR(p, seg, niter, kmax, lambda, ecartmin, ecartmax, minReads, adaptNbrIterations, vSeed = -1, saveAsRDS = FALSE, dirOut = "out")
p |
a |
seg |
a |
niter |
a positive |
lambda |
a positive |
minReads |
a positive |
adaptNbrIterations |
a |
vSeed |
a |
saveAsRDS |
a |
kMax |
a positive |
minInterval |
a |
maxInterval |
a |
maxLength |
a positive |
0.
Pascal Belleau, Astrid Deschenes
## Load synthetic dataset of reads data(syntheticNucleosomeReads) ## Use dataset of reads to create GRanges object sampleGRanges <- GRanges(seqnames = syntheticNucleosomeReads$dataIP$chr, ranges = IRanges(start = syntheticNucleosomeReads$dataIP$start, end = syntheticNucleosomeReads$dataIP$end), strand = syntheticNucleosomeReads$dataIP$strand) # Segmentation of the reads seg <- segmentation(sampleGRanges, zeta = 147, delta = 50, maxLength = 1000) ## Not run: dir.create("out") dir.create("out/done") dir.create("out/results") runCHR(p=1, seg=seg, niter=1000, kmax=330,lambda=3, ecartmin=147, ecartmax=297, minReads=5) ## End(Not run)