funtooNorm

funtooNorm normalizes DNA methylation data from the Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K) to account for cell-type and tissue-specific variability in methylation patterns.

Key Features:

• Implementation: Implemented as an R package.
• Cell-Type Flexibility: Builds upon the funNorm method, enhancing flexibility for handling data from diverse cell and tissue types.
• Optimal Component Selection: Provides a visual display of cross-validated errors to aid determination of the optimal number of components for normalization.
• Demonstrated Performance: Demonstrates substantial improvements across three distinct datasets and performs well on chromosome X where methylation shows unique inter-tissue variability.

Scientific Applications:

• Epigenetic studies across tissues: Normalizes Illumina 450K methylation data from multiple cell or tissue types to enable comparative epigenomic analyses.
• Mixed-sample analyses: Enables normalization of datasets containing mixed cell-type or tissue samples to preserve biologically meaningful methylation variation.
• Chromosome X methylation analysis: Addresses inter-tissue variability specific to chromosome X methylation patterns.

Methodology:

Extends the funNorm normalization method and uses cross-validation to display errors for selecting the optimal number of normalization components for Illumina 450K methylation data.