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The ALLELE Procedure |
A marker locus M can have a series of alleles ,
. A sample of
individuals can therefore have several different genotypes at the locus, with
copies of type
. The number
of copies of allele
can be found directly by summation:
. The sample frequencies are written as
and
. The
’s are unbiased maximum likelihood estimates (MLEs) of the population proportions
.
The variance of the sample allele frequency is calculated as
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and can be estimated by replacing and
with their sample values
and
. The variance of the sample genotype frequency
is not generally calculated; instead, an MLE of the HWD coefficient
for alleles
and
is calculated as
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and the MLE’s variance is estimated using one of the following formulas, depending on whether the two alleles are the same or different:
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The standard error, the square root of the variance, is reported for the sample allele frequencies and the disequilibrium coefficient estimates. When the BOOTSTRAP= option of the PROC ALLELE statement is specified, bootstrap confidence intervals are formed by resampling individuals from the data set and are reported for these estimates, with the % confidence level given by the ALPHA=
option (or
by default).
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Copyright © 2008 by SAS Institute Inc., Cary, NC, USA. All rights reserved.