methmage: MethMAGE test

In MethylCapSig: Detection of Differentially Methylated Regions using MethylCap-Seq Data

Description

Calculates a generalized estimating equation (GEE) based test statistic as used in MethMAGE package.

Usage

methmage(X, Y)

Arguments

X	A matrix of dimension n \times k whose rows represent the samples collected from n individuals from the first group on k variates.
Y	A matrix of dimension m \times k whose rows correspond to samples collected from m individuals from the second group on k variates.

Details

methmage uses a generalized estimating equations (GEE) approach to test for equality of mean vectors for two groups of multivariate observations. Using a first order autoregressive (AR(1)) structure as the working correlation matrix, methmage uses geeglm function from the geepack package to estimate the coefficients and construct the test statistic. To ensure convergence in modest time, maximum number of iterations and convergence criterion (epsilon) are set at 100 and 10^{-8} respectively.

Value

A 2 \times 1 vector consisting of the test statistic and the p-value.

Author(s)

Deepak N. Ayyala, David E. Frankhouser

References

Frankhouser, D. E., et al. (2014) PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data, Bioinformatics, 30 (24), 3567 – 3574.

Examples

data(diffMethylData)
methmage(diffMethylData$region1.x, diffMethylData$region1.y)
# methmage(diffMethylData$region2.x, diffMethylData$region2.y)

MethylCapSig documentation built on May 2, 2019, 9:24 a.m.