methylCC

methylCC estimates cell-type composition from whole blood DNA methylation (DNAm) data in a technology-independent manner to account for intra-sample cellular heterogeneity.

Key Features:

• Technology independence: Provides cell composition estimation that is applicable across multiple DNAm measurement platforms including Illumina 450K microarray, whole genome bisulfite sequencing (WGBS), and reduced representation bisulfite sequencing (RRBS).
• Whole blood focus: Targets estimation of proportions of constituent cell types within whole blood DNAm samples.
• Mitigation of platform-specific bias: Produces consistent cell composition estimates across technologies to reduce technology-specific biases in downstream analyses.
• Implementation: Distributed as an R/Bioconductor package for integration into R-based analysis workflows.
• Control of cellular heterogeneity: Explicitly addresses intra-sample cellular heterogeneity that can confound DNAm association studies.

Scientific Applications:

• Cell composition deconvolution: Estimating proportions of blood cell types from DNAm data for studies using whole blood samples.
• Confounding adjustment in epigenetic association studies: Adjusting for cellular heterogeneity to reduce false positives and confounding in DNAm-outcome associations.
• Cross-technology comparisons: Enabling consistent cell composition estimates for comparative analyses across Illumina 450K, WGBS, and RRBS datasets.

Methodology:

Implemented as an R/Bioconductor package that performs technology-independent estimation of cell type composition from whole blood DNAm data applicable to Illumina 450K microarray, WGBS, and RRBS.