genotypeEmissionCrlmm {VanillaICE} | R Documentation

## Estimate the emission probabilities using confidence scores from CRLMM

### Description

Estimate the emission probabilities that incorporate information on the confidence scores for the genotype calls.

### Usage

    genotypeEmissionCrlmm(genotypes, conf, pHetCalledHom = 0.001, pHetCalledHet = 0.995, pHomInNormal = 0.99, pHomInRoh = 0.999, annotation)

### Arguments

`genotypes` | Matrix of genotypes
`conf` | Matirx of confidence scores (see details).
`pHetCalledHom` | The probability that a truly heterozygous SNP is incorrectly called homozygous (incorrect call).
`pHetCalledHet` | The probability that a truly heterozygous SNP is called heterozygous (correct call).
`pHomInNormal` | The probability of a homozygous genotype call in the 'normal' state.
`pHomInRoh` | The probability of a homozygous genotype call in a region of homozygosity.
`annotation` | The cdf name (e.g., "genomewidesnp6")

### Details

The confidence scores by crlmm are saved as an integer: 1000*log(1-p), where p is the probability that the genotype call is correct.

The reference distribution of confidence scores are available for the following Affymetrix platforms: affy6, nsp250, and sty250k.

### Value

An R x C x X array of emission probabilities, where
R = number of loci (SNPs) C = number of samples S = number of states

### Author(s)

R Scharpf

### References

RB Scharpf et al. (2008), Annals of Applied Statistics

[Package VanillaICE version 1.6.0 Index]