callEmission {VanillaICE} | R Documentation

## Calculate emission probabilities for the ICE HMM

### Description

When confidence estimates are incorporated in the ICE HMM for genotype calls, the observed data at a SNP is the genotype call and the uncertainty measure. The joint distribution of the call and the uncertainty measure depends on the underlying hidden state. This function calculates the emission probability for the joint sequence of calls and confidence scores. See reference for additioal details.

### Usage

    callEmission(object, P.CHOM.Normal, P.CHOM.LOH, SAMPLE=1)

### Arguments

`object` | An object inheriting from `AnnotatedSnpSet`
`P.CHOM.Normal` | probability of called homozygous given the true underlying state is normal (retention of heterozygosity)
`P.CHOM.LOH` | probability of called homozygous given the true underlying state is loss of heterozygosity
`SAMPLE` | Integer: which sample

### Details

This function is essentially a wrapper for `getHapmapProbabilities` that allows the object to contain the merged 50k Xba and Hind chips, or the merged 250k Nsp and Sty chips. Because the distribution of the uncertainty estimates are chip-specific (enzyme-specific), this function computes enzyme-specific emission probabilities (note: one of the columns in `featureData` must have the name 'enzyme' and the elements in the vector must be 'Xba' and 'Hind' or 'Nsp' and 'Sty'.).

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

### Note

### Author(s)

### References

### See Also

`getHapmapProbabilities`, `crlmm`, `featureData` For the callsConfidence package, see http://www.biostat.jhsph.edu/~rscharpf/software/index.html

### Examples

      data(chromosome1)
      ##Create an object of class AnnotatedSnpCallSet
      callset <- new("AnnotatedSnpSet",
                     calls=calls(chromosome1),
                     callsConfidence=callsConfidence(chromosome1),
                     featureData=featureData(chromosome1),
                     phenoData=phenoData(chromosome1),
                     annotation=annotation(chromosome1))
      ##1 = homozygous (AA or BB), 2 = heterozygous
      calls(callset)[calls(callset) == 3] <-  1
      ##make sure that enzyme information is stored in featureData

    ## Not run:
      require("callsConfidence")
        emissionProb <- callEmission(object=callset,
                                     P.CHOM.Normal=0.70,
                                     P.CHOM.LOH=0.999)
        range(emissionProb)
    ## End(Not run)

[Package VanillaICE version 1.0.2 Index]