Finds blocks of methylation differences for Illumina methylation arrays
Methods for function 'bumphunter' in Package 'minfi'
Estimates A/B compartments from Illumina methylation arrays
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.
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
Multi-dimensional scaling plots giving an overview of similarities and differences between samples.
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
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