calculateDiffMethDSS {methylKit} | R Documentation

## calculate Differential Methylation with DSS

### Description

This function provides an interface to the beta-binomial model from DSS package by Hao Wu. It calculates the differential methylation statistics using a beta-binomial model with parameter shrinkage. See the reference for details.

### Usage

    calculateDiffMethDSS(meth, adjust = c("SLIM", "holm", "hochberg",
      "hommel", "bonferroni", "BH", "BY", "fdr", "none", "qvalue"),
      mc.cores = 1)

    ## S4 method for signature 'methylBase'
    calculateDiffMethDSS(meth, adjust = c("SLIM",
      "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none",
      "qvalue"), mc.cores = 1)

### Arguments

`meth` | a methylBase object
`adjust` | different methods to correct the p-values for multiple testing. Default is "SLIM" from methylKit. For "qvalue" please see `qvalue` and for all other methods see `p.adjust`.
`mc.cores` | integer denoting how many cores should be used for parallel differential methylation calculations (can only be used in machines with multiple cores).

### Value

a methylDiff object

### References

Feng H, Conneely K and Wu H (2014). A bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data. Nucleic acids research

### Examples

    data(methylKit)

    dssDiffay <- calculateDiffMethDSS(methylBase.obj, adjust="SLIM", mc.cores=1)

[Package methylKit version 1.12.0 Index]