reads_demo_02: Forward reads and reverse reads in 'GRanges' format (for demo...

In ArnaudDroitLab/RJMCMCNucleosomes: Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)

Description

A group of forward and reverse reads that can be used to test the rjmcmc function.

Usage

data(reads_demo_02)

Format

A GRanges containing forward and reverse reads.

Value

A GRanges containing forward and reverse reads.

See Also

• 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.

Examples

## 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)

ArnaudDroitLab/RJMCMCNucleosomes documentation built on May 5, 2019, 7:06 a.m.