getHapmapProbabilities {VanillaICE} | R Documentation

## Estimate probability of correct genotype call

### Description

This function is used by the ICE HMM described in the reference below and currently only supported for 50k and 250k Affymetrix SNP chips. A nonparametric estimate of the probability that the genotype call is correct is based on the distribution of `crlmm` confidence scores in the reference HapMap population, where we assume that we know the true genotype. A similar approach could be used to estimate probabilities with other genotyping algorithms. See reference below for more information.

### Usage

    getHapmapProbabilities(object)

### Arguments

`object` | One of the HMM classes defined in `ICE`

### Details

The annotation slot in the object must contain one of the following strings that identifies the Affymetrix chip:

mapping100k (if the 50k xba and 50k hind results have been merged into one object)

pd.mapping50k.xba240 (50k Xba platform)

pd.mapping50k.hind240 (50k Hind)

mapping500k (if the two 250k chips – Nsp and Sty – have been merged)

pd.mapping250k.nsp

pd.mapping250k.sty

### Value

A vector of probabilities that the genotype call is correct.

### Note

Estimated probabilities are chip-specific. This function is typically not called directly.

### Author(s)

### References

RB Scharpf et al. (2007), Department of Biostatistics Working Papers, Working Paper 136

### See Also

`callEmission`, `crlmm`

### Examples

[Package VanillaICE version 1.0.2 Index]