getCallEmission {VanillaICE} | R Documentation

## Calculates emission probabilities for genotype calls

### Description

Calculates emission probabilities for genotype calls. Only used by the ICE HMM.

### Usage

    getCallEmission(object, CALL.STATES = 2, SAMPLE = 1, P.HOM.CHOM = 0.999,
    P.HET.CHOM = 1 - 0.999, P.HET.CHET = 0.999, P.HOM.CHET = 1 - 0.999,
    P.CHOM.Normal, P.CHOM.LOH, hapmapP)

### Arguments

`object` | Typically an object of class `HmmSnpCallSet`
`CALL.STATES` | Integer: number of hidden states (default is 2 – loss of heterozygosity and retention of heterozygosity)
`SAMPLE` | Integer: which sample to extract genotype calls from the `HmmSnpCallSet` object
`P.HOM.CHOM` | Numeric. Probability that the true genotype is homozygous (AA or BB) given that the observed genotype was homozygous (AA or BB)
`P.HET.CHOM` | Numeric. Probability that the true genotype is heterozygous (AB) given that the observed genotype was homozygous.
`P.HET.CHET` | Numeric. Probability that the true genotype is heterozygous (AB) given that the observed genotype was heterozygous.
`P.HOM.CHET` | Numeric. Probability that the true genotype is homozygous given that the observed genotype was heterozygous.
`P.CHOM.Normal` | Numeric. Probability that the observed genotype is homozygous if the true hidden state is retention of heterozygosity.
`P.CHOM.LOH` | Numeric. Probability that the observed genotype is homozygous given that the true hidden state is loss of heterozygosity.
`hapmapP` | A matrix estimated from 269 HapMap samples. See details.

### Details

We group the CRLMM probabilities of a correct genotype call for the 269 HapMap samples into 1 of 4 possible categories:

1: genotype call is HET, truth is HOM 2: genotype call is HET, truth is HET 3: genotype call is HOM, truth is HOM 4: genotype call is HOM, truth is HET

### Value

Returns matrix of emission probabilities that are a function of the confidence scores provided by `crlmm` for genotype calls.

### Note

Not typically called directly.

### Author(s)

### References

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

### See Also

The R package callsConfidence: http://www.biostat.jhsph.edu/~rscharpf/software/index.html

`callEmission`, `hmm`, `crlmm`

### Examples

[Package VanillaICE version 1.0.2 Index]