Sib-pair Command: multihomoz


ClassAnalysis and data manipulation command
Namemultihomoz
Arguments [<binary trait> [|<quantitative trait> >|>=|<|<=|==|^= <threshold>]]

Prints the asymptotic Z statistic and a one-sided MC P-value for whether the maximum length of runs of homozygosity at marker loci along the specified map is increased in probands, either affected if the trait is binary, or above or below the given threshold if the trait is quantitative.

Example:

>> include linclex.in
>> multihomoz lincl

-------------------------------------------------------
Runs of marker homozygosity in cases of trait "lincl"
-------------------------------------------------------

Length of runs of homozygosity that include a given marker

Marker           Mean run  Minimum run  Expected run     Variance  Z-statistic
--------------  ---------  -----------  ------------  -----------  -----------
D13S162               2.1            0           0.4          0.0      11.55
D13S160               2.2            0           0.2          0.0      13.75
D13S170               2.0            0           0.1          0.0      17.03
--------------  ---------  -----------  ------------  -----------  -----------
Best over all         2.2            0           0.5          0.0      13.56

     Marker Set          Aff  Nmark Obs-Run Exp-Run    Z    Emp P  Iters
--------------------- ------ ------ ------- ------- ------ ------  -----
  D13S162 - D13S170       12      3     2.3     0.9   6.08 0.0050    201 HOM-Run *

>> set iterations 10000
>> set plevel 1
>> multihomoz lincl

-------------------------------------------------------
Runs of marker homozygosity in cases of trait "lincl"
-------------------------------------------------------

Markers: D13S162 D13S160 D13S170

Pedigree  ID         Run  Homozygosity pattern
--------- ---------- ---- --------------------
1         3             3 111
1         4             3 111
2         7             3 111
2         8             3 111
3         9             1 100
3         11            3 111
4         3             2 110
6         3             1 101
8         4             3 111
9         4             1 010
10        4             2 011
...

      No. usable observations =     12      ( 16.7%)
      Mean homozyg run length =      2.3333 out of    3
      Best homozyg run length =      2.1667 for "D13S160"

Length of runs of homozygosity that include a given marker

Marker           Mean run  Minimum run  Expected run     Variance  Z-statistic
--------------  ---------  -----------  ------------  -----------  -----------
D13S162               2.1            0           0.4          0.0      10.77
D13S160               2.2            0           0.2          0.0      13.68
D13S170               2.0            0           0.1          0.0      17.22
--------------  ---------  -----------  ------------  -----------  -----------
Best over all         2.2            0           0.5          0.0      12.81

    Mean (Var) simulated runs =      0.8865 (      0.0521)
                  Z statistic =      6.3402
      Equalled or exceeded by =   1/10001 simulated values (0.0001)


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