| reads_demo_02 {RJMCMCNucleosomes} | R Documentation |
GRanges format
(for demo purpose).A group of forward and reverse reads that can be used to test the
rjmcmc function.
data(reads_demo_02)
A GRanges containing forward and reverse reads.
A GRanges containing forward and reverse reads.
rjmcmc for profiling of nucleosome positions
rjmcmcCHR for profiling of nucleosome positions
for a large region. The function will take care of spliting and
merging.
segmentation for spliting a GRanges
containing reads in a list of smaller segments for
the rjmcmc function.
postTreatment for merging closely positioned
nucleosomes
mergeRDSFiles for merging nucleosome information
from selected RDS files.
plotNucleosomes for generating a graph containing
the nucleosome positions and the read coverage.
## Loading dataset
data(reads_demo_02)
## Nucleosome positioning
## Since there is only one chromosome present in reads_demo_02, the name
## of the chromosome does not need to be specified
rjmcmc(reads = reads_demo_02, nbrIterations = 150, lambda = 3, kMax = 30,
minInterval = 144, maxInterval = 290, minReads = 6)