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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