mma: Selective phenotyping with similarity measure 2

Description

Selective phenotyping with similarity measure 2 to select the most dissimilar subset of individuals.

Usage

mma(genof, p, sequent = FALSE, exact = FALSE, dismat = FALSE)

Value

A list containing cList, dismat if that option is

TRUE and further optimized lists (op, op2,

moment2) if sequent is TRUE. vector as the first item. The list of items includes:

cList: vector of selected subjects by function mma
op: list containing vector of selection and update flag from function op
op2: matrix of selection by function op2
moment2: vector of second moment calculations
dismat: dissimilarity matrix

Arguments

genof: Genotype matrix.
p: Sample size to select.
sequent: Perform sequential optimization if TRUE (see below).
exact: Count allele differences if FALSE; binary 0 = same number of alleles, 1 = different if TRUE.
dismat: Return dissimilarity matrix if TRUE.

Author

Brian S. Yandell (mailto:byandell@wisc.edu)

Details

Sequentially minimize 1st moment and then 2nd moment, swapping one subject at a time. op finds all the samples with same 1st moment similarity with mma results. op2 finds all the samples with the same 1st moment similarity with every list from op result. A combination of op and op2 comes very close to exhaustive search in practice. moment2 find the best list with minimum 2nd moments from the output of op2. Note that some warnings occurs accompanying our return statement. The results are not affected though.

This function combines several functions in Jin's original code. mma(genof,p,sequent=TRUE is identical to the depricated mmasequent(genof,p. mma(genof,p,exact=TRUE is identical to the depricated mmaM1(genof,p (actually, mma uses dissimilarity while mmaM1 used similarity = 1 - dissimilarity).

References

Jin C, Lan H, Attie AD, Churchill GA, Bulutuglo D, Yandell BS (2004) Selective phenotyping for increased efficiency in genetic mapping studies. Genetics 168: 2285-2293.