crlmm

The "crlmm" R package addresses the challenges of analyzing genotype-phenotype and copy number-phenotype associations using genotyping platforms like Affymetrix. While existing genotyping algorithms generally agree when analyzing HapMap samples, methods for assessing copy number changes show more variability and discordance. A significant factor contributing to this inconsistency is the susceptibility of copy number estimates to systematic differences arising from variations in sample processing across different times or labs, known as batch effects.

"crlmm" tackles this issue head-on by implementing a sophisticated multilevel model that adjusts for batch effects and provides allele-specific estimates of copy number. This approach significantly enhances the reliability of copy number analysis by mitigating the risk of spurious associations caused by unaccounted-for batch effects.

Furthermore, "crlmm" facilitates a comprehensive workflow for estimating allele-specific copy numbers. It integrates marker-level estimates with complementary Bioconductor software, enabling the inference of regions of copy number gain or loss within R's versatile statistical computing environment.