Sib-pair Command: mito|yhap


ClassAnalysis and data manipulation command
Namemito | 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


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