VanillaICE

"VanillaICE" is an R package to detect and analyze a wide range of chromosomal DNA alterations using high-density single nucleotide polymorphism (SNP) microarrays. Recognizing the significance of chromosomal variations—from entire chromosome alterations such as aneuploidy to segmental changes and minor genomic region modifications including single nucleotide polymorphisms (SNPs)—VanillaICE employs Hidden Markov Models (HMMs) to model the spatial dependence between neighboring SNPs. This approach is adept at identifying changes in copy number (deletions and duplications) and genotype (e.g., regions of homozygosity), which are crucial for understanding normal genetic variation and disease mechanisms.

VanillaICE enhances previous HMM-based methods by integrating copy number and genotype calls along with corresponding measures of uncertainty. This integration allows for more accurate and robust detection of chromosomal alterations. Through applying confidence scores, VanillaICE effectively controls smoothing within a probabilistic framework, improving the inference of SNP array data.