chromosome1 {VanillaICE} | R Documentation

## Simulated chromosome 1

### Description

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

### Usage

    data(chromosome1)

### Details

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.

### References

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

### Examples

    data(chromosome1)
    chromosome1

[Package VanillaICE version 1.2.0 Index]