| Class | Analysis and data manipulation command |
| Name | mito | yhap |
| Arguments | hap | <quantitative trait> [cat] | <quantitative trait> [<marker 1> [...<marker N>]]. |
Performs ANOVA (contingency chi-square) analysis of the association between a quantitative (binary or categorical) trait and Y chromosome or mitochondrial haplotypes, defaulting to each eligible marker in turn if markers making up a haplotype are not explicitly listed. Haplotypes are imputed where unequivocal, and Monte-Carlo empiric P-values are produced by gene-dropping.
If hap has been specified, then the counts of the haplotypes are tabulated.
Example:
set loc a haploid set loc b qua read ped inline 1 1 x x m 3/3 12 1 2 x x f x/x 8 1 3 1 2 f x/x 8 1 4 1 2 m 3/3 8 1 5 1 2 m 3 3 2 2 1 x x m 2/2 15 2 2 x x f x/x x 2 3 1 2 m x/x 10 2 4 1 2 m x/x 16 ;;;; run set plevel 1 yhap b
>> include mito.in
>> lis pop
Locus Type Position
--------------- ---- ----------------
pop q 6 1=CEU 2=ASW 3=MEX 4=TSI
>> mit pop cat $h
------------------------------------------------------
Association of trait "pop" with Mito haplotypes
------------------------------------------------------
Mit-Markers: rs2001030-rs3928306-rs2853497-rs2854122-rs28359178-rs28357684-rs2854125
Mother-offspring inconsistency due to M019--NA19733
Haplotype 1 2 3 4 Total
-----------------------------------------------------------------------------------------------
A-G-G-C-A-G-C 2 (.013) 0 (.000) 1 (.014) 0 (.000) 3
A-G-G-C-G-G-C 5 (.031) 0 (.000) 0 (.000) 1 (.013) 6
A-G-G-T-G-G-C 0 (.000) 11 (.155) 0 (.000) 1 (.013) 12
G-A-A-C-A-G-C 1 (.006) 0 (.000) 0 (.000) 0 (.000) 1
G-A-G-C-A-G-C 8 (.050) 0 (.000) 0 (.000) 4 (.053) 12
G-A-G-C-A-G-T 0 (.000) 0 (.000) 0 (.000) 1 (.013) 1
G-A-G-C-G-G-C 29 (.181) 0 (.000) 1 (.014) 11 (.147) 41
G-A-G-C-G-G-T 0 (.000) 0 (.000) 0 (.000) 1 (.013) 1
G-A-G-T-G-A-C 0 (.000) 2 (.028) 10 (.141) 1 (.013) 13
G-G-A-T-G-G-C 0 (.000) 1 (.014) 29 (.408) 0 (.000) 30
G-G-A-T-G-G-T 0 (.000) 8 (.113) 1 (.014) 0 (.000) 9
G-G-G-C-A-G-C 6 (.037) 0 (.000) 0 (.000) 3 (.040) 9
G-G-G-C-G-A-C 1 (.006) 0 (.000) 0 (.000) 0 (.000) 1
G-G-G-C-G-G-C 101 (.631) 1 (.014) 18 (.254) 49 (.653) 169
G-G-G-C-G-G-T 0 (.000) 0 (.000) 2 (.028) 1 (.013) 3
G-G-G-T-A-G-C 0 (.000) 2 (.028) 0 (.000) 0 (.000) 2
G-G-G-T-G-A-C 0 (.000) 0 (.000) 6 (.085) 0 (.000) 6
G-G-G-T-G-A-T 1 (.006) 0 (.000) 0 (.000) 0 (.000) 1
G-G-G-T-G-G-C 6 (.037) 46 (.648) 3 (.042) 2 (.027) 57
-----------------------------------------------------------------------------------------------
No. trait(+) marker(-) = 59
No. trait(+) marker(+) = 377
Contingency Pearson chi-sq = 511.8
Nominal degrees of freedom = 19
Nominal P-value = 0.0000
Equalled or exceeded by =1/201 simulated values (0.0050)
Mean (Var) simulated chi-sqs = 61.7 ( 163.3)
See also:
| test haploid | Check Mendel errors |
| << (assoc) | Up to index | >> (rare) |