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)