oxBS.MLE: oxBS-MLE.

In USCbiostats/ENmixUSC: Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip (USC version)

Description

Find the 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 measurements (proportions of methylated signals in total signals) obtained from bisulfite (BS) experiments
beta.oxBS	A matrix of measurements obtained from oxidative bisulfite (oxBS) experiments
N.BS	A matrix of total signals 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 order of rows/columns in all four matrices should be consistent (otherwise oxBS.MLE will stop with error messages). Using a binomial model at each CpG locus in each sample, oxBS.MLE outputs a list with two matrices: a matrix of MLEs of 5mC levels and a matrix of MLEs of 5hmC levels. The rows and columns of both matrices are consistent with the rows and columns of the input matrices. For any CpG locus in any sample, if any of the four corresponding 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

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, under review.

Examples

# load example data
load(system.file("oxBS.MLE.RData",package="ENmix"))
# run oxBS.MLE
temp<-oxBS.MLE(beta.BS,beta.oxBS,N.BS,N.oxBS)

USCbiostats/ENmixUSC documentation built on June 1, 2019, 3:55 a.m.