mma {qtlDesign} | R Documentation |
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)
Arguments
genof |
Genotype matrix. |
p |
Sample size to select. |
sequent |
Perform sequential optimization if TRUE (see below). |
exact |
Count allele differences if |
dismat |
Return dissimilarity matrix if TRUE. |
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).
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 |
Author(s)
Brian S. Yandell (mailto:byandell@wisc.edu)
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.