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. |
getAdjusted |
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 |
gsameth |
Generalised gene set testing for Illumina's methylation array 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 |
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 |