Class | Analysis and data manipulation command |
Name | mcfrequency |
Arguments | <codominant marker> | $m. |
Print MCEM (Monte-Carlo Expectation-Maximization) estimates of the founder allele frequencies for marker loci. A fixed number of EM iterations are carried out, usually 20. This can be set higher if desired using the set emit command.
When all individuals genotyped are unrelated, then the maximum likelihood estimates of the allele frequencies in the population from which the sample are drawn are simply the sample frequencies. This is also asymptotically true for data from related individuals. So, for large datasets, the naive counting estimates that Sib-pair usually uses approach the MLEs. For smaller samples of families, these estimates can be improved upon. The MCEM algorithm Sib-pair offers seems to give answers very similar to those obtained by numerically maximizing the pedigree likelihood.
Example:
>> include volgaex.in >> set iterations 200 >> set timer on # # Naive estimates of marker frequencies # >> fre D14S52 ------------------------------------------------ Allele frequencies for locus "D14S52" ------------------------------------------------ Allele Frequency Count Histogram 57 0.0238 1 * 69 0.0238 1 * 81 0.0476 2 * 83 0.4286 18 ********* 85 0.1905 8 **** 87 0.2381 10 ***** 93 0.0476 2 * Number of alleles = 7 Heterozygosity (Hu) = 0.7352 Poly. Inf. Content = 0.6763 4 Neff mu (SSMM) = 4.88968079 Number persons typed = 21 ( 27.3%) [ 0.00 s] # # Maximum likelihood estimates of marker frequencies # >> mcf D14S52 ------------------------------------------------ MCEM allele frequencies for locus "D14S52" ------------------------------------------------ Allele Frequency Count Histogram 57 0.0495 2 * 69 0.0422 2 * 81 0.0411 2 * 83 0.4938 19 ********** 85 0.0820 3 ** 87 0.2489 9 ***** 93 0.0425 2 * Number of alleles = 7 Heterozygosity (Hu) = 0.6981 Poly. Inf. Content = 0.6405 4 Neff mu (SSMM) = 3.69111229 Number of founders = 19 ( 2.6% typed) [ 11.84 s]
For the same data, the maximum likelihood estimates from MENDEL 7.0 are:
LOCUS ALLELE ESTIMATED STANDARD NAME NAME FREQUENCY ERROR D14S52 57 0.0431 0.0422 D14S52 69 0.0431 0.0422 D14S52 81 0.0431 0.0422 D14S52 83 0.4950 0.1072 D14S52 85 0.0822 0.0639 D14S52 87 0.2505 0.0915 D14S52 93 0.0431 0.0422
See also:
blup | BLUE allele frequency |
<< (frequencies) | Up to index | >> (count) |