To cite package ‘VanillaICE’ in publications use:

  Hidden Markov models for the assessment of chromosomal alterations
  using high-throughput SNP arrays R.B. Scharpf and G. Parmigiani and
  J. Pevsner and I. Ruczinski 2008, Annals of Applied Statistics

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Robert B. Scharpf and Giovanni Parmigiani and Jonathan Pevsner and Ingo Ruczinski},
    title = {Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays},
    journal = {Annals of Applied Statistics},
    year = {2008},
  }