RJMCMC_result: Nucleosomes obtained by running RJMCMC function using reads...

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

Description

A list of class "rjmcmcNucleosomes" which contains the information about the detected nucleosomes.

Usage

data(RJMCMC_result)

Format

A list of class "rjmcmcNucleosomes" containing:

• call the matched call.

• k a integer, the final estimation of the number of nucleosomes. 0 when no nucleosome is detected.

• mu a vector of numeric of length k, the positions of the nucleosomes. NA when no nucleosome is detected.

• k_max a integer, the maximum number of nucleosomes obtained during the iteration process. NA when no nucleosome is detected.

Value

A list of class "rjmcmcNucleosomes" containing:

• call the matched call.

• k a integer, the final estimation of the number of nucleosomes. 0 when no nucleosome is detected.

• mu a vector of numeric of length k, the positions of the nucleosomes. NA when no nucleosome is detected.

• k_max a integer, the maximum number of nucleosomes obtained during the iteration process. NA when no nucleosome is detected.

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(RJMCMC_result)
data(reads_demo_02)

## Results before post-treatment
RJMCMC_result$mu

## Post-treatment function which merged closely positioned nucleosomes
postResult <- postTreatment(reads = reads_demo_02,
    extendingSize = 60, chrLength = 100000, resultRJMCMC = RJMCMC_result)

## Results after post-treatment
postResult

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