test.allele.switch {snpStats} | R Documentation

## Test for switch of alleles between two collections

### Description

When testing genotype data derived from different platforms or scoring algorithms a common problem is switching of alleles. This function provides a diagnostic for this. Input can either be two objects of class `"SnpMatrix"` to be examined, column by column, for allele switching, or a single `"SnpMatrix"` object together with an indicator vector giving group membership for its rows.

### Usage

    test.allele.switch(snps, snps2 = NULL, split = NULL, prior.df = 1)

### Arguments

`snps` | An object of class `"SnpMatrix"` or `"XSnpMatrix"`
`snps2` | A second object of the same class as `snps`
`split` | If only one `SnpMatrix` object supplied, a vector with the same number of elements as rows of `snps`. It must be capable of coercion to a factor with two levels.
`prior.df` | A degree of freedom parameter for the prior distribution of the allele frequency `prior.df` (see Details)

### Details

This function calculates a Bayes factor for the comparison of the hypothesis that the alleles have been switched with the hypothesis that they have not been switched. This requires integration over the posterior distribution of the allele frequency. The prior is taken as a beta distribution with both parameters equal to `prior.df`so that the prior is symmetric about 0.5. The default, `prior.df=1` represents a uniform prior on (0,1).

### Value

A vector containing the log (base 10) of the Bayes Factors for an allele switch.

### Author(s)

David Clayton dc208@cam.ac.uk

### See Also

`SnpMatrix-class`, `XSnpMatrix-class`

### Examples

    data(testdata)
    #
    # Call with two SnpMatrix arguments
    #
    cc <- as.numeric(subject.data$cc)
    lbf1 <- test.allele.switch(Autosomes[cc==1,], Autosomes[cc==2,])
    #
    # Single matrix call (giving the same result)
    #
    lbf2 <- test.allele.switch(Autosomes, split=cc)

[Package snpStats version 1.40.0 Index]