methylKit (version 0.99.2)

calculateDiffMethDSS: 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 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

# NOT RUN {
data(methylKit)

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

# }