# Analysing Illumina HumanMethylation BeadChip Data

## Documentation for package ‘missMethyl’ version 1.42.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

missMethyl-package | Introduction to the missMethyl package
contrasts.varFit | Compute contrasts for a varFit object.
densityByProbeType | Plot the beta value distributions of the Infinium I and II probe types relative to the overall beta value distribution.
getAdj | Extract values adjusted for unwanted variation by RUVm
getINCs | Extract intensity data for Illumina negative controls found on 450k or EPIC arrays.
getLeveneResiduals | Obtain Levene residuals
getMappedEntrezIDs | Get mapped Entrez Gene IDs from CpG probe names
gometh | Gene ontology testing for Ilumina methylation array data
goregion | Gene ontology testing of DMRs for Ilumina methylation array data
gsameth | Generalised gene set testing for Illumina's methylation array data
gsaregion | Generalised gene set testing for Illumina's methylation array data
gsaseq | Generalised gene set testing for RNA-seq data
missMethyl | Introduction to the missMethyl package
RUVadj | RUV adjust
RUVfit | Remove unwanted variation when testing for differential methylation
SWAN | Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips
SWAN.default | Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips
SWAN.MethyLumiSet | Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips
SWAN.RGChannelSet | Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips
topGSA | Get table of top 20 enriched pathways
topRUV | Table of top-ranked differentially methylated CpGs obatained from a differential methylation analysis using RUV
topVar | Table of top-ranked differentially variable CpGs
varFit | Testing for differential variability
varFit.default | Testing for differential variability
varFit.DGEList | Testing for differential variability
varFit.MethylSet | Testing for differential variability