skewr

skewr generates visualization and quality-control plots for Illumina Human Methylation 450k BeadChip methylation intensity and Beta-value distributions.

Key Features:

• Nine-plot panel: Produces a comprehensive panel of nine plots for assessing methylation intensity distributions and Beta-values.
• Density plots: Creates six density plots of methylated and unmethylated intensities across three probe subsets (Type I-red, Type I-green, Type II).
• Beta-value distributions: Generates three Beta-value distributions corresponding to Type I-red, Type I-green, and Type II probes, where Beta-values are the ratio of methylated probe intensity to overall intensity.

Scientific Applications:

• Quality Control: Visualizes intensity and Beta-value distributions to identify anomalies or biases such as batch effects or technical artifacts in Illumina 450k data.
• Data Exploration: Enables characterization of the methylation landscape across probe types to support downstream analyses.

Methodology:

Implemented in the R programming language and distributed within the Bioconductor framework.