MLINK: impossible result?

Frank Visser fvisser at hgmp.mrc.ac.uk
Fri Aug 18 10:02:47 EST 1995


I. Fenton (ifenton at hgmp.mrc.ac.uk) wrote:
: [snip, snip - discussion of possibly weird mlink result]

: my random thoughts... could the DATAIN.DAT file be posted, so that
: we can see exactly how the disease and/or liability classes have
: been set up.  there may be something subtle in there that you're
: not spotting.  also a lod-score table and/or PEDIN.DAT may help us.

OK, here follows:

datain.dat:

--------

 4   0   0   1 << no loci, risk locus, sexlinked(if 1)
 0  0.0  0.0  0  << mut locus, mut rate, haplotype freq(if 1)
 1 2 3 4  << order of loci
 
 1  2  << affectation, # alleles [CHED]
  9.9900000000E-01   1.0000000000E-03  << gene freqs
 1 << number of liability classes
 0.000  1.000  1.000  << genotype penetrances
 
 2  4  << binary factors, # alleles [114 ]
  6.0000000000E-02   8.1000000000E-01   1.0000000000E-02   
1.2000000000E-01  << gene freqs
 4  << number of binary factors
1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
 
 2  5  << binary factors, # alleles [48  ]
  2.5000000000E-01   3.0000000000E-01   1.3000000000E-01   
1.9000000000E-01   1.3000000000E-01  << gene freqs
 5  << number of binary factors
1 0 0 0 0
0 1 0 0 0
0 0 1 0 0
0 0 0 1 0
0 0 0 0 1
 
 2  5  << binary factors, # alleles [471 ]
  1.7000000000E-01   2.5000000000E-01   1.0000000000E-01   
3.0000000000E-01   1.8000000000E-01  << gene freqs
 5  << number of binary factors
1 0 0 0 0
0 1 0 0 0
0 0 1 0 0
0 0 0 1 0
0 0 0 0 1
 
 0  0  << sex difference (if 1) and interference (if 1)
 0.0  0.0  0.0  << recombination values
 1   << this locus may have iterated values
 1 1 1

-----
and pedfile.dat

----
1  1  0  0  4  0  0 1 1  1  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 1
1  2  0  0  4  0  0 2 0  2  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 2
1  3  0  0  8  0  0 1 0  1  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 3
1  4  1  2  8  6  6 2 0  2  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 4
1  5  0  0 10  0  0 1 0  1  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 5
1  6  1  2 10  0  0 2 0  2  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 6
1  7  0  0 13  0  0 1 0  1  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 7
1  8  3  4 13  0  0 2 0  2  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 8
1  9  0  0 22  0  0 1 0  1  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 9
1 10  5  6 22 12 12 2 0  2  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 10
1 11  0  0 23  0  0 1 0  1  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 11
1 12  5  6 23  0  0 2 0  2  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 12
1 13  7  8 26 16 16 1 0  2  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 13
1 14  0  0 26  0  0 2 0  1  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 14
1 15  0  0 27  0  0 1 0  1  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 15
1 16  7  8 27 18 18 2 0  2  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 16
1 17  0  0 33  0  0 1 0  1  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 17
1 18  7  8 33 20 20 2 0  2  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 18
1 19  0  0 36  0  0 1 0  1  1 1 0 0  0 0 1 1 0  0 1 0 1 0  Ped: 1  Per: 19
1 20  7  8 36  0  0 2 0  2  1 0 0 1  0 1 0 0 1  0 1 1 0 0  Ped: 1  Per: 20
1 21  0  0 39  0  0 1 0  1  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 21
1 22  9 10 39  0  0 2 0  2  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 22
1 23 11 12 40  0  0 1 0  2  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 23
1 24  0  0 40  0  0 2 0  1  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 24
1 25  0  0 42  0  0 1 0  1  0 1 0 1  1 1 0 0 0  0 0 0 1 0  Ped: 1  Per: 25
1 26 13 14 42  0  0 2 0  2  1 0 0 0  0 0 0 0 1  0 1 1 0 0  Ped: 1  Per: 26
1 27 15 16 44 29 29 1 0  2  0 0 1 1  0 1 1 0 0  0 1 0 0 1  Ped: 1  Per: 27
1 28  0  0 44  0  0 2 0  1  0 1 0 0  0 0 0 0 0  0 1 0 1 0  Ped: 1  Per: 28
1 29 15 16  0 31 31 1 0  1  0 0 0 1  0 1 0 1 0  0 0 1 0 1  Ped: 1  Per: 29
1 30  0  0 46  0  0 1 0  1  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 30
1 31 15 16 46  0  0 2 0  2  0 0 1 1  0 1 1 0 0  1 1 0 0 0  Ped: 1  Per: 31
1 32  0  0 48  0  0 1 0  1  0 1 0 0  1 1 0 0 0  0 1 0 0 0  Ped: 1  Per: 32
1 33 17 18 48 35 35 2 0  2  1 0 1 0  0 0 0 1 1  1 1 0 0 0  Ped: 1  Per: 33
1 34  0  0 54  0  0 1 0  1  0 1 0 0  1 1 0 0 0  1 0 1 0 0  Ped: 1  Per: 34
1 35 17 18 54  0  0 2 0  2  1 0 1 0  0 0 0 1 1  0 1 0 0 1  Ped: 1  Per: 35
1 36 19 20  0 37 37 2 0  2  1 1 0 0  0 0 0 1 1  0 1 0 0 0  Ped: 1  Per: 36
1 37 19 20  0  0  0 2 0  1  0 1 0 1  0 1 0 1 0  0 1 1 0 0  Ped: 1  Per: 37
1 38  0  0 56  0  0 1 0  1  0 0 0 0  0 0 0 0 0  0 0 0 0 0  Ped: 1  Per: 38
1 39 21 22 56  0  0 2 0  2  1 0 0 1  0 1 0 0 1  0 1 0 1 0  Ped: 1  Per: 39
1 40 23 24  0 41 41 1 0  2  1 1 0 0  0 0 0 1 1  0 1 0 1 0  Ped: 1  Per: 40
1 41 23 24  0  0  0 2 0  1  0 1 0 1  0 1 0 1 0  0 1 1 0 0  Ped: 1  Per: 41
1 42 25 26  0 43 43 1 0  1  1 0 0 1  0 1 0 0 1  0 0 1 1 0  Ped: 1  Per: 42
1 43 25 26  0  0  0 2 0  2  1 1 0 0  1 0 0 0 1  0 1 0 1 0  Ped: 1  Per: 43
1 44 27 28  0 45 45 2 0  2  0 1 1 0  1 0 1 0 0  0 1 0 0 0  Ped: 1  Per: 44
1 45 27 28  0  0  0 1 0  1  0 1 0 1  0 1 0 1 0  0 1 0 0 1  Ped: 1  Per: 45
1 46 30 31  0 47 47 1 0  2  0 0 1 1  0 0 1 1 0  0 1 0 0 1  Ped: 1  Per: 46
1 47 30 31  0  0  0 2 0  1  0 1 0 1  1 1 0 0 0  1 0 0 1 0  Ped: 1  Per: 47
1 48 32 33  0 50 50 1 0  1  0 1 1 0  0 1 0 1 0  1 1 0 0 0  Ped: 1  Per: 48
1 49  0  0 59  0  0 1 0  1  0 1 0 0  0 0 1 0 1  0 0 0 1 1  Ped: 1  Per: 49
1 50 32 33 59 51 51 2 0  2  1 1 0 0  1 0 0 0 1  0 1 0 0 0  Ped: 1  Per: 50
1 51 32 33  0 53 53 2 0  2  1 1 0 0  0 1 0 0 1  0 1 0 0 0  Ped: 1  Per: 51
1 52  0  0 62  0  0 1 0  1  0 1 0 0  1 0 0 1 0  0 0 0 1 1  Ped: 1  Per: 52
1 53 32 33 62  0  0 2 0  2  1 1 0 0  1 0 0 0 1  0 1 0 0 0  Ped: 1  Per: 53
1 54 34 35  0 55 55 1 0  1  0 1 1 0  1 0 0 1 0  1 0 0 0 1  Ped: 1  Per: 54
1 55 34 35  0  0  0 2 0  2  1 1 0 0  0 0 0 0 0  1 1 0 0 0  Ped: 1  Per: 55
1 56 38 39 64 58 58 1 0  2  1 0 1 0  0 0 1 0 1  0 1 0 1 0  Ped: 1  Per: 56
1 57  0  0 64  0  0 2 0  1  0 1 0 1  0 1 1 0 0  1 0 0 0 0  Ped: 1  Per: 57
1 58 38 39  0  0  0 2 0  1  0 0 1 1  0 1 1 0 0  0 1 0 0 0  Ped: 1  Per: 58
1 59 49 50  0 60 60 2 0  1  0 1 0 0  1 0 1 0 0  0 1 0 0 1  Ped: 1  Per: 59
1 60 49 50  0 61 61 2 0  1  0 1 0 0  1 0 1 0 0  0 1 0 0 1  Ped: 1  Per: 60
1 61 49 50  0  0  0 1 0  1  0 1 0 0  1 0 1 0 0  0 1 0 0 1  Ped: 1  Per: 61
1 62 52 53  0 63 63 2 0  2  1 1 0 0  0 0 0 1 1  0 0 0 0 0  Ped: 1  Per: 62
1 63 52 53  0  0  0 2 0  1  0 1 0 0  0 0 0 0 0  0 1 0 1 0  Ped: 1  Per: 63
1 64 56 57  0  0  0 2 0  2  1 1 0 0  0 0 1 0 1  1 0 0 1 0  Ped: 1  Per: 64

-----

and the final results, as displayed by lrp:

----

Order      0.0    0.05     0.1    0.15     0.2
-----  ------- ------- ------- ------- -------
1=4       3.39    5.05    4.66    4.14    3.55  a


-----

All suggestions welcome.

Frank




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