oxBS.MLE: oxBS-MLE.

In ENmix: Quality control and analysis tools for Illumina DNA methylation BeadChip

Description

Maximum Likelihood Estimate (MLE) of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) using sequencing/array data from paired bisulfite and oxidative bisulfite treated DNA experiments.

Usage

oxBS.MLE(beta.BS,beta.oxBS,N.BS,N.oxBS)

Arguments

beta.BS	A matrix of methylation beta values (proportion of methylated sites estimated as methylated intensity over total intensity) obtained from bisulfite (BS) experiments
beta.oxBS	A matrix of methylation beta values obtained from oxidative bisulfite (oxBS) experiments
N.BS	A matrix of total signals (sum of methylated and unmethylated intensity values) from BS experiments
N.oxBS	A matrix of total signals from oxBS experiments

Details

For all the inputs (beta.BS, beta.oxBS, N.BS and N.oxBS), the rows should be corresponding to CpG loci and the columns should be corresponding to samples. The row/column names in all four matrices should be the same. For a specific CpG of a sample, if any one of the four values (beta.BS, beta.oxBS, N.BS and N.oxBS) is NA, or N.BS is zero, or N.oxBS is zero, the MLE of both 5mC and 5hmC levels will be set as NA.

Value

The output is a list with two elements: 5mC: a matrix of estimated 5mC levels. 5hmC: a matrix for estimated 5hmC levels.

Author(s)

Liang Niu and Zongli Xu

References

Zongli Xu, Jack A. Taylor, Yuet-Kin Leung, Shuk-Mei Ho and Liang Niu, oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA, Bioinformatics. 2016

Examples

# load example data
load(system.file("oxBS.MLE.RData",package="ENmix"))
# run oxBS.MLE
resu<-oxBS.MLE(beta.BS,beta.oxBS,N.BS,N.oxBS)
dim(resu[["5mC"]])
dim(resu[["5hmC"]])

ENmix documentation built on April 2, 2021, 6 p.m.