hapmapProbabilities {VanillaICE} | R Documentation

## CRLMM confidence scores on HapMap data

### Description

Wrapper for extracting the chip-specific distribution of CRLMM confidence scores for HapMap data where we assume we know the true genotype. Presently only supported for Affymetrix 50k and 250k SNP chips and onnly relevant for fitting the ICE HMM (see reference below).

### Usage

    hapmapProbabilities(x)

### Arguments

`x` | Name of chip. Must be 'pd.mapping...'

### Details

Confidence scores in a `SnpCallSet` created by `crlmm` are stored in the element "pAcc" in the assay data.

### Value

Matrix of confidence scores

### Note

### Author(s)

### References

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

### See Also

`crlmm`, `SnpCallSet-class`, `AssayDataElement`

### Examples

[Package VanillaICE version 1.0.2 Index]