snpStats (version 1.22.0)

test.allele.switch: 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)

Value

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

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.dfso that the prior is symmetric about 0.5. The default, prior.df=1 represents a uniform prior on (0,1).

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)