ChAMP
The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.
- Bioconductor
- https://bioconductor.org/packages/ChAMP
Source attribution
- Bioconductor — ChAMP
Related resources
Precise measurements are important for epigenome-wide studies investigating DNA methylation in whole blood samples, where effect sizes are expected to be small in magnitude. The 450K platform is often affected by batch effects and proper preprocessing is recommended. This package provides functions to read and normalize 450K '.idat' files. The normalization corrects for dye bias and biases related to signal intensity and methylation of probes using local regression. No adjustment for probe type bias is performed to avoid the trade-off of precision for accuracy of beta-values.
Tools for quanlity control, analysis and visulization of Illumina DNA methylation array data.
A fast scatterplot smoother based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available.
Tools to analyze & visualize Illumina Infinium methylation arrays.
Identification of diferentially methylated regions (DMRs) in predefined regions (promoters, CpG islands...) from the human genome using Illumina's 450K or EPIC microarray data. Provides methods to rank CpG probes based on linear models and includes plotting functions.