GenomicMethylSet instances
GenomicRatioSet instances
Class 'IlluminaMethylationAnnotation'
Class '"IlluminaMethylationManifest"'
MethylSet instances
Class '"RGChannelSet"'
RatioSet instances
Finds blocks of methylation differences for Illumina methylation arrays
Methods for function 'bumphunter' in Package 'minfi'
Estimates A/B compartments from Illumina methylation arrays
Plot control probe signals.
Collapse methylation values of adjacent CpGs into a summary value.
Density bean plots of methylation Beta values.
Density plots of methylation Beta values.
Detection p-values for all probed genomic positions.
Find differentially methylated positions
Cell Proportion Estimation
Fix methylation outliers
Find gap signals in 450k data
Accessing annotation for Illumina methylation objects
Reading Illumina methylation array data from GEO.
Estimate sample-specific quality control (QC) for methylation data
Estimating sample sex based on methylation data
logit in base 2.
Make a GenomicRatioSet from a matrix
Mapping methylation data to the genome
Multi-dimensional scaling plots giving an overview of similarities and differences between samples.
Analyze Illumina's methylation arrays
easy one-step QC of methylation object
Plot the overall distribution of beta values and the distributions of the Infinium I and II probe types.
Plot methylation values at an single genomic position
Functional normalization for Illumina 450k arrays
Perform preprocessing as Genome Studio.
The Noob background correction for 450k arrays.
Stratified quantile normalization for an Illumina methylation array.
Creation of a MethylSet without normalization
Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips
QC report for Illumina Infinium Human Methylation 450k arrays
Converting methylation signals to ratios (Beta or M-values)
Parsing IDAT files from Illumina methylation arrays.
Reads an entire 450k experiment using a sample sheet
Reading an Illumina methylation sample sheet
Read in Unmethylated and Methylated signals from a GEO raw file.
Read in tab deliminited file in the TCGA format
Various utilities