oxBS.MLE {ENmix} | R Documentation

## oxBS-MLE.

### 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"]])

[Package ENmix version 1.28.8 Index]