hummingbird-package {hummingbird} | R Documentation

## A Bayesian Hidden Markov Model for the detection of differentially methylated regions

### Description

A package for identifying differentially methylated regions (DMRs) between case and control groups using whole genome bisulfite sequencing (WGBS) or reduced representative bisulfite sequencing (RRBS) experiment data.

The hummingbird package uses a Bayesian hidden Markov model (HMM) for detecting DMRs. It fits a Bayesian HMM for one chromosome at a time. The final output of hummingbird are the detected DMRs with start and end positions in a given chromosome, directions of the DMRs (hyper- or hypo-), and the numbers of CpGs in these DMRs.

The hummingbird package implements the algorithm described in the publication below.

### Details

The main functions of the package are: hummingbirdEM, hummingbirdPostAdjustment and hummingbirdGraph.

### Author(s)

Eleni Adam, Tieming Ji, Desh Ranjan

Maintainer: Eleni Adam <eadam002@odu.edu>

### References

Ji (2019) A Bayesian hidden Markov model for detecting differentially methylated regions. Biometrics 75(2):663-673.

[Package hummingbird version 1.2.0 Index]