Analysis of methylation array data


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Documentation for package ‘missMethyl’ version 1.4.0

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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.
getINCs Extract intensity data for 613 Illumina negative controls found on 450k arrays.
getLeveneResiduals Obtain Levene residuals
gometh Gene ontology testing for 450K methylation data
missMethyl Introduction to the missMethyl package
RUVadj Adjust estimated variances
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
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