chromosome1            package:VanillaICE            R Documentation

_S_i_m_u_l_a_t_e_d _c_h_r_o_m_o_s_o_m_e _1

_D_e_s_c_r_i_p_t_i_o_n:

     Simulated genotype calls and copy number estimates for chromosome
     1 (Affymetrix 100k platform).

_U_s_a_g_e:

     data(chromosome1)

_D_e_t_a_i_l_s:

     The simulation comprises one subject's genotype, copy number, and
     confidences scores for 9165 SNPs on chromosome 1.  A description
     of the 5 features simulated in chromosome 1, referred to by
     regions A-E, and the underlying hidden states in these regions
     follows.

     Genotype calls: With the exception of three regions in this
     chromosome, we simulated 9165 genotypes (the approximate number of
     SNPs in the two 50k SNP chips) from a Bernoulli distribution with
     probability 0.7 of a homozygous genotype.  Confidence scores for
     genotype estimates were obtained by random draws of confidence
     scores in the Hapmap data when the CRLMM genotype calls agreed
     with the gold-standard as defined by consensus of the HapMap
     genotyping centers. 

     Copy number: The Affymetrix CNAT tool (version 3.0) was used to
     obtain copy number estimates for the 9165 SNPs from a presumably
     normal individual in the HapMap dataset (sample identifier
     NA06993).  Deletions and amplificatons were simulated from
     Gaussian distributions with location parameters log2(1) and
     log2(3), respectively.  For the scale parameter, we used a robust
     estimate of the log2 transformed copy number standard deviation. 
     To illustrate how a confidence score such as a standard error of
     the copy number estimate could be useful, we simulated standard
     errors from a shifted Gamma: Gamma(1, 2) + 0.3, where 1 is the
     shape parameter and 2 is the rate parameter.  To ascertain the
     effect of qualitatively high confidence scores on the ICE HMM, we
     scaled the robust standard deviation estimate by 1/2. Similarly,
     to simulate less precise copy number estimates, we multiplied the
     robust standard deviation estimate by a factor of 2.

     For additional information on the five abnormalities simulated in
     this chromosome, see the manuscript referenced below.

_R_e_f_e_r_e_n_c_e_s:

     RB Scharpf et al. (2008) Hidden Markov Models for the assessment
     of chromosomal alterations using high-throughput SNP arrays,
     Annals of Applied Statistics

_E_x_a_m_p_l_e_s:

     data(chromosome1)
     chromosome1

