crlmm

crlmm estimates allele-specific copy number and genotypes from Affymetrix SNP 5.0 and 6.0 arrays and Illumina platforms while adjusting for batch effects.

Key Features:

• Batch Effect Adjustment: Implements a multilevel model to adjust for batch effects in genotyping and array data.
• Allele-Specific Copy Number Estimation: Provides allele-specific copy-number estimates from marker-level probe intensities.
• Integration with Bioconductor: Produces marker-level estimates that can be integrated with Bioconductor packages to infer regions of copy-number gain or loss.
• Statistical Environment R: Operates within the R statistical environment.

Scientific Applications:

• High-resolution CNV analysis: Performs allele-specific CNV analysis on Affymetrix SNP 5.0/6.0 and Illumina array data, applicable to large datasets.
• Genotype–phenotype association studies: Reduces spurious associations by adjusting for batch effects in genotype–phenotype and copy-number–phenotype analyses.
• Disease genetics and CNV discovery: Supports investigation of CNV contributions to complex traits and disease mechanisms via accurate allele-specific estimates.

Methodology:

Uses a multilevel modeling approach to correct batch effects and estimates allele-specific copy numbers from marker-level intensities; results can be integrated with Bioconductor tools to identify regions of genomic gain or loss.