SNPMClust (version 1.3)

generatepriors: Generate pseudodata for snpmclust

Description

Generates bivariate normal pseudodata for the homozygous and heterozygous minor genotypes.

Usage

generatepriors(x, y, calls, priorpoints = length(x) * 0.2, xm1 = NA, xm2 = NA, xm3 = NA, ym1 = NA, ym2 = NA, ym3 = NA, ranseed = ranseed)

Arguments

x

x-vector of signal intensity data in transformed scale.

y

y-vector of signal intensity data in transformed scale.

calls

A priori genotype calls for intensity data.

priorpoints

The number of observations of pseudodata to be generated for the heterozygous and homozygous minor genotypes.

xm1, xm2, xm3, ym1, ym2, ym3

Pseudodata cluster means can be user-specified through these parameters. The ordered pair (xm1,ym1) gives the cluster mean for genotype AA; similarly for (xm2,ym2), (xm3,ym3) and AB, BB, respectively. Default values are NA, in which case cluster means are estimated from the data, conditional on the a priori genotypes passed via calls.

ranseed

Random seed for generation of pseudodata. The default is 1969.

Value

A priorpoints-by-2 matrix.

References

Stephen W. Erickson, Joshua Callaway (2016). SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays. Journal of Statistical Software, 71(2), 1-9. doi:10.18637/jss.v071.c02