Sib-pair Command: fstats


ClassAnalysis and data manipulation command
Namefstats
Arguments <binary trait> |<quantitative trait> [founders]

Prints the F statistics comparing identity-by-state sharing of alleles within loci, within populations (demes), and between populations. Population membership of an individual is indicated by the value of a specified binary or quantitative trait. There can be more than two populations, and must be more than one population.

The statistics are:

FIS = (HS-HO)/HS,

FIT = (HT-HO)/HT,

FST = (HT-HS)/HT.

These estimates are derived via the approach of Pons and Chaouche [1995], as described by Excoffier [2001], replacing the heterozygosities with estimates:

HO*Unweighted mean observed deme heterozygosity
HS*Expected deme heterozygosity
HT*Expected total heterozygosity

The results actually are actually generated via assoc, so the usual Pearson contingency chi-square with aymptotic and gene-dropping P-values testing for between-population allele frequency differences are also generated. The summary output is organised differently.

Example:

>> fst pop

--------------------------------------------------
F-statistics for populations "pop"
--------------------------------------------------
Population membership indicator:
pop                  x:    0     1.0:   80     2.0:   40     3.0:   40

Marker         Typed  Allels  Pops   Fis    Fit    Fst  Asy P  Emp P  Iters
-------------- ------ ------ ----- ------ ------ ------ ------ ------ ------
Loc1              160      2     3 -.0351 0.5055 0.5223 0.0000 0.0050    201 Fstat ***
Loc2              120      3     3 -.1161 0.8393 0.8560 0.0000 0.0050    201 Fstat ***
Loc3              140      2     3 0.0045 0.0033 -.0012 0.4493 0.5128     39 Fstat .
--------------                     ------ ------ ------
Multilocus                         -.0254 0.5347 0.5462


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