tmle.npvi

tmle.npvi performs integrative genome-wide analysis to identify associations between DNA copy number variations (CNVs) and gene expression while adjusting for DNA methylation.

Key Features:

• Integrative analysis: Searches for genomic regions where CNVs associate with gene expression while accounting for DNA methylation.
• Genome-wide application: Applies the analysis across the entire genome for large-scale studies.
• Targeted-search method implementation: Implements the Chambaz et al. (2012) targeted-search framework for detecting regions with significant associations.
• Application in breast cancer: Demonstrated use in breast cancer to identify regions with joint CNV, expression, and methylation associations.

Scientific Applications:

• Cancer genomics: Identifies complex interactions among CNVs, gene expression, and DNA methylation relevant to cancer development and progression.
• Epigenetic studies: Supports analysis of how DNA methylation modulates the relationship between CNVs and gene expression.

Methodology:

Implements the Chambaz et al. (2012) targeted-search framework to identify genomic regions with significant CNV–expression associations while incorporating DNA methylation in genome-wide analyses.