regions from beta-valued methylation data
Authors: KOYEL MAJUMDAR, ISOBEL CLAIRE GORMLEY, THOMAS BRENDAN MURPHY, ROMINA SILVA, ANTOINETTE SABRINA PERRY, RONALD WILLIAM WATSON, FLORENCE JAFFR ́EZIC, ANDREA RAU
A hidden Markov model approach for identifying differentially methylated sites and regions for beta-valued DNA methylation data. The workflow consists of 3 main functions: \itemize{ \item betaHMM: to estimate the hidden Markov model parameters and the hidden methylation states of each CpG sites. \item dmc_identification: uses the output from the above function to identify CpG sites that are mostly differentially methylated between DNA samples collected from \eqn{R} conditions. \item dmr_identification: to identify adjacent DMCs forming DMRs. }
A typical call to betaHMM to apply the Baum-Welch algorithm and Viterbi algorithm takes the following form:
library(betaHMM)
### read the methylation file and annotation file
data(sample_methylation_file)
head(sample_methylation_file)
data(sample_annotation_file)
head(sample_annotation_file)
betaHMM_out <- betaHMM(sample_methylation_file,
sample_annotation_file,
M = 3,
N = 4,
R = 2,
parallel_process = FALSE,
seed = 321,
treatment_group = c("Benign","Tumour"))
where M
represents the number of methylation state in a DNA sample, N
represents the number of subjects or DNA replicates, R
represents the number
of conditions from where DNA is extracted.
A typical call to dmc_identification takes the following form:
dmc_out <- dmc_identification(betaHMM_out)
dmc_df <- assay(dmc_out)
A typical call to dmr_identification takes the following form:
dmr_out <- dmr_identification(dmc_out)
dmr_df <- assay(dmr_out)
The output of the betaHMM
function is an
S4 object of class betaHMMResults
, the output of the dmc_identification
function is an S4 object of class dmcResults
and the output of the
dmr_identification
function is an S4 object of class dmrResults
on which standard plot
and summary
functions can be directly applied;
the former uses functionalities from the
ggplot2 package.
The betaHMM package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, as published by the Free Software Foundation.
This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.
A copy of the GNU General Public License, version 3, is available at http://www.r-project.org/Licenses/GPL-3.