question on the practice of LINKAGE program
YMMCS023 at TWNMOE10.Edu.TW
YMMCS023 at TWNMOE10.Edu.TW
Wed Apr 20 07:53:46 EST 1994
Dear Friends,
Would you please tell me someone who has experience using LINKAGE and is intere
sted in teaching a "LINKAGE newhand" through e-mail? Because it's difficult fo
r me to attend the LINKAGE courses in a year.
I tried to run two pedigrees from the paper for Huntington's disease by Gusella
(Nature 306:234-238, 1983). I successfully "calculated" out the lod score of th
e American pedigree but failed to run the Venerian pedigree. There was always a
"run time error" even with repeated check of the input data. The following is
pedigree file and parameter file I used. Would you please let someone check it
for me? Thanks.
Venerian pedigree (I failed to analyze this pedigree with LINKAGE)
.pre file
1 1 0 0 1 2 0 0
1 2 0 0 2 1 0 0
1 3 1 2 2 2 0 0
1 4 0 0 1 1 0 0
1 5 1 2 2 2 0 0
1 6 0 0 1 1 0 0
1 7 4 3 2 2 0 0
1 8 0 0 1 1 0 0
1 9 4 3 2 2 0 0
1 10 0 0 1 1 0 0
1 11 6 5 1 2 0 0
1 12 0 0 2 1 0 0
1 13 8 7 2 2 0 0
1 14 0 0 1 1 0 0
1 15 10 9 1 2 0 0
1 16 0 0 2 1 1 2
1 17 11 12 2 2 0 0
1 18 0 0 1 1 0 0
1 19 11 12 2 2 0 0
1 20 0 0 1 1 0 0
1 21 11 12 1 1 1 1
1 22 11 12 1 2 0 0
1 23 0 0 2 1 0 0
1 24 14 13 2 1 1 1
1 25 14 13 2 1 1 2
1 26 14 13 2 2 0 0
1 27 0 0 1 1 0 0
1 28 15 16 2 2 0 0
1 29 15 16 1 1 1 2
1 30 15 16 1 1 1 2
1 31 18 17 2 2 2 3
1 32 18 17 2 1 1 2
1 33 18 17 1 1 1 2
1 34 18 17 2 1 1 2
1 35 20 19 1 1 1 2
1 36 20 19 2 2 2 3
1 37 20 19 2 1 1 2
1 38 20 19 2 1 1 2
1 39 20 19 1 2 2 3
1 40 20 19 2 1 2 2
1 41 20 19 1 2 2 3
1 42 20 19 1 2 1 3
1 43 20 19 1 1 1 1
1 44 22 23 1 2 2 3
1 45 22 23 2 1 3 4
1 46 22 23 2 1 2 2
1 47 22 23 1 2 2 3
1 48 27 26 1 2 1 3
1 49 0 0 2 1 1 2
1 50 27 26 2 2 1 3
1 51 27 26 2 2 1 3
1 52 27 26 2 1 1 3
1 53 27 26 2 2 1 3
1 54 27 26 1 1 1 1
1 55 29 28 1 2 2 3
1 56 0 0 2 1 1 1
1 57 29 28 1 1 1 1
1 58 29 28 1 2 2 3
1 59 29 28 2 1 1 1
1 60 39 40 1 2 2 3
1 61 39 40 1 2 2 3
1 62 44 45 1 2 3 3
1 63 48 49 1 2 1 3
1 64 48 49 1 2 2 3
1 65 55 56 2 2 2 3
.ped file, after MAKEPED .pre
1 1 0 0 3 0 0 1 1 2 0 0 Ped: 1 Per: 1
1 2 0 0 3 0 0 2 0 1 0 0 Ped: 1 Per: 2
1 3 1 2 7 5 5 2 0 2 0 0 Ped: 1 Per: 3
1 4 0 0 7 0 0 1 0 1 0 0 Ped: 1 Per: 4
1 5 1 2 11 0 0 2 0 2 0 0 Ped: 1 Per: 5
1 6 0 0 11 0 0 1 0 1 0 0 Ped: 1 Per: 6
1 7 4 3 13 9 9 2 0 2 0 0 Ped: 1 Per: 7
1 8 0 0 13 0 0 1 0 1 0 0 Ped: 1 Per: 8
1 9 4 3 15 0 0 2 0 2 0 0 Ped: 1 Per: 9
1 10 0 0 15 0 0 1 0 1 0 0 Ped: 1 Per: 10
1 11 6 5 17 0 0 1 0 2 0 0 Ped: 1 Per: 11
1 12 0 0 17 0 0 2 0 1 0 0 Ped: 1 Per: 12
1 13 8 7 24 0 0 2 0 2 0 0 Ped: 1 Per: 13
1 14 0 0 24 0 0 1 0 1 0 0 Ped: 1 Per: 14
1 15 10 9 28 0 0 1 0 2 0 0 Ped: 1 Per: 15
1 16 0 0 28 0 0 2 0 1 1 2 Ped: 1 Per: 16
1 17 11 12 31 19 19 2 0 2 0 0 Ped: 1 Per: 17
1 18 0 0 31 0 0 1 0 1 0 0 Ped: 1 Per: 18
1 19 11 12 35 21 21 2 0 2 0 0 Ped: 1 Per: 19
1 20 0 0 35 0 0 1 0 1 0 0 Ped: 1 Per: 20
1 21 11 12 0 22 22 1 0 1 1 1 Ped: 1 Per: 21
1 22 11 12 44 0 0 1 0 2 0 0 Ped: 1 Per: 22
1 23 0 0 44 0 0 2 0 1 0 0 Ped: 1 Per: 23
1 24 14 13 0 25 25 2 0 1 1 1 Ped: 1 Per: 24
1 25 14 13 0 26 26 2 0 1 1 2 Ped: 1 Per: 25
1 26 14 13 48 0 0 2 0 2 0 0 Ped: 1 Per: 26
1 27 0 0 48 0 0 1 0 1 0 0 Ped: 1 Per: 27
1 28 15 16 55 29 29 2 0 2 0 0 Ped: 1 Per: 28
1 29 15 16 55 30 30 1 0 1 1 2 Ped: 1 Per: 29
1 30 15 16 0 0 0 1 0 1 1 2 Ped: 1 Per: 30
1 31 18 17 0 32 32 2 0 2 2 3 Ped: 1 Per: 31
1 32 18 17 0 33 33 2 0 1 1 2 Ped: 1 Per: 32
1 33 18 17 0 34 34 1 0 1 1 2 Ped: 1 Per: 33
1 34 18 17 0 0 0 2 0 1 1 2 Ped: 1 Per: 34
1 35 20 19 0 36 36 1 0 1 1 2 Ped: 1 Per: 35
1 36 20 19 0 37 37 2 0 2 2 3 Ped: 1 Per: 36
1 37 20 19 0 38 38 2 0 1 1 2 Ped: 1 Per: 37
1 38 20 19 0 39 39 2 0 1 1 2 Ped: 1 Per: 38
1 39 20 19 60 40 40 1 0 2 2 3 Ped: 1 Per: 39
1 40 20 19 60 41 41 2 0 1 2 2 Ped: 1 Per: 40
1 41 20 19 0 42 42 1 0 2 2 3 Ped: 1 Per: 41
1 42 20 19 0 43 43 1 0 2 1 3 Ped: 1 Per: 42
1 43 20 19 0 0 0 1 0 1 1 1 Ped: 1 Per: 43
1 44 22 23 62 45 45 1 0 2 2 3 Ped: 1 Per: 44
1 45 22 23 62 46 46 2 0 1 3 4 Ped: 1 Per: 45
1 46 22 23 0 47 47 2 0 1 2 2 Ped: 1 Per: 46
1 47 22 23 0 0 0 1 0 2 2 3 Ped: 1 Per: 47
1 48 27 26 63 50 50 1 0 2 1 3 Ped: 1 Per: 48
1 49 0 0 63 0 0 2 0 1 1 2 Ped: 1 Per: 49
1 50 27 26 0 51 51 2 0 2 1 3 Ped: 1 Per: 50
1 51 27 26 0 52 52 2 0 2 1 3 Ped: 1 Per: 51
1 52 27 26 0 53 53 2 0 1 1 3 Ped: 1 Per: 52
1 53 27 26 0 54 54 2 0 2 1 3 Ped: 1 Per: 53
1 54 27 26 0 0 0 1 0 1 1 1 Ped: 1 Per: 54
1 55 29 28 65 57 57 1 0 2 2 3 Ped: 1 Per: 55
1 56 0 0 65 0 0 2 0 1 1 1 Ped: 1 Per: 56
1 57 29 28 0 58 58 1 0 1 1 1 Ped: 1 Per: 57
1 58 29 28 0 59 59 1 0 2 2 3 Ped: 1 Per: 58
1 59 29 28 0 0 0 2 0 1 1 1 Ped: 1 Per: 59
1 60 39 40 0 61 61 1 0 2 2 3 Ped: 1 Per: 60
1 61 39 40 0 0 0 1 0 2 2 3 Ped: 1 Per: 61
1 62 44 45 0 0 0 1 0 2 3 3 Ped: 1 Per: 62
1 63 48 49 0 64 64 1 0 2 1 3 Ped: 1 Per: 63
1 64 48 49 0 0 0 1 0 2 2 3 Ped: 1 Per: 64
1 65 55 56 0 0 0 2 0 2 2 3 Ped: 1 Per: 65
.dat file, in PREPLINK
2 0 0 5 << NO. OF LOCI, RISK LOCUS, SEXLINKED (IF 1) PROGRAM
0 0.0 0.0 0 << MUT LOCUS, MUT MALE, MUT FEM, HAP FREQ (IF 1)
1 2
1 2 << AFFECTION, NO. OF ALLELES
0.9990 1.00000E-03 << GENE FREQUENCIES
1 << NO. OF LIABILITY CLASSES
0.0000 1.0000 1.0000 << PENETRANCES
3 4 << ALLELE NUMBERS, NO. OF ALLELES
0.6878 0.1667 0.0833 0.0625 << GENE FREQUENCIES
0 0 << SEX DIFFERENCE, INTERFERENCE (IF 1 OR 2)
0.00500 << RECOMBINATION VALUES
1 0.10000 0.45000 << REC VARIED, INCREMENT, FINISHING VALUE
American pedigree (It's OK to analyze this pedigree with LINKAGE)
.pre file
1 1 0 0 2 2 0 0
1 2 0 0 1 1 0 0
1 3 2 1 2 2 0 0
1 4 0 0 1 1 0 0
1 5 2 1 1 2 0 0
1 6 0 0 2 1 0 0
1 7 2 1 2 2 0 0
1 8 0 0 1 1 0 0
1 9 4 3 2 2 0 0
1 10 0 0 1 1 1 2
1 11 4 3 2 1 1 2
1 12 4 3 2 2 0 0
1 13 0 0 1 1 0 0
1 14 4 3 2 2 0 0
1 15 0 0 1 1 0 0
1 16 4 3 2 2 0 0
1 17 0 0 1 1 0 0
1 18 4 3 1 1 1 2
1 19 5 6 1 1 2 4
1 20 5 6 2 1 1 2
1 21 8 7 1 2 1 1
1 22 0 0 2 1 1 4
1 23 8 7 1 2 0 0
1 24 0 0 2 1 1 1
1 25 8 7 1 1 1 3
1 26 8 7 1 1 1 3
1 27 10 9 1 2 1 2
1 28 0 0 2 1 1 3
1 29 10 9 1 2 1 2
1 30 13 12 1 2 1 1
1 31 13 12 1 2 1 1
1 32 13 12 1 1 1 1
1 33 15 14 2 2 1 2
1 34 17 16 2 2 1 1
1 35 21 22 2 2 1 1
1 36 21 22 1 2 1 4
1 37 23 24 2 2 1 1
1 38 23 24 2 2 1 1
1 39 23 24 1 2 1 1
1 40 27 28 1 2 1 3
.ped file
1 1 0 0 3 0 0 2 0 2 0 0 Ped: 1 Per: 1
1 2 0 0 3 0 0 1 1 1 0 0 Ped: 1 Per: 2
1 3 2 1 9 5 5 2 0 2 0 0 Ped: 1 Per: 3
1 4 0 0 9 0 0 1 0 1 0 0 Ped: 1 Per: 4
1 5 2 1 19 7 7 1 0 2 0 0 Ped: 1 Per: 5
1 6 0 0 19 0 0 2 0 1 0 0 Ped: 1 Per: 6
1 7 2 1 21 0 0 2 0 2 0 0 Ped: 1 Per: 7
1 8 0 0 21 0 0 1 0 1 0 0 Ped: 1 Per: 8
1 9 4 3 27 11 11 2 0 2 0 0 Ped: 1 Per: 9
1 10 0 0 27 0 0 1 0 1 1 2 Ped: 1 Per: 10
1 11 4 3 0 12 12 2 0 1 1 2 Ped: 1 Per: 11
1 12 4 3 30 14 14 2 0 2 0 0 Ped: 1 Per: 12
1 13 0 0 30 0 0 1 0 1 0 0 Ped: 1 Per: 13
1 14 4 3 33 16 16 2 0 2 0 0 Ped: 1 Per: 14
1 15 0 0 33 0 0 1 0 1 0 0 Ped: 1 Per: 15
1 16 4 3 34 18 18 2 0 2 0 0 Ped: 1 Per: 16
1 17 0 0 34 0 0 1 0 1 0 0 Ped: 1 Per: 17
1 18 4 3 0 0 0 1 0 1 1 2 Ped: 1 Per: 18
1 19 5 6 0 20 20 1 0 1 2 4 Ped: 1 Per: 19
1 20 5 6 0 0 0 2 0 1 1 2 Ped: 1 Per: 20
1 21 8 7 35 23 23 1 0 2 1 1 Ped: 1 Per: 21
1 22 0 0 35 0 0 2 0 1 1 4 Ped: 1 Per: 22
1 23 8 7 37 25 25 1 0 2 0 0 Ped: 1 Per: 23
1 24 0 0 37 0 0 2 0 1 1 1 Ped: 1 Per: 24
1 25 8 7 0 26 26 1 0 1 1 3 Ped: 1 Per: 25
1 26 8 7 0 0 0 1 0 1 1 3 Ped: 1 Per: 26
1 27 10 9 40 29 29 1 0 2 1 2 Ped: 1 Per: 27
1 28 0 0 40 0 0 2 0 1 1 3 Ped: 1 Per: 28
1 29 10 9 0 0 0 1 0 2 1 2 Ped: 1 Per: 29
1 30 13 12 0 31 31 1 0 2 1 1 Ped: 1 Per: 30
1 31 13 12 0 32 32 1 0 2 1 1 Ped: 1 Per: 31
1 32 13 12 0 0 0 1 0 1 1 1 Ped: 1 Per: 32
1 33 15 14 0 0 0 2 0 2 1 2 Ped: 1 Per: 33
1 34 17 16 0 0 0 2 0 2 1 1 Ped: 1 Per: 34
1 35 21 22 0 36 36 2 0 2 1 1 Ped: 1 Per: 35
1 36 21 22 0 0 0 1 0 2 1 4 Ped: 1 Per: 36
1 37 23 24 0 38 38 2 0 2 1 1 Ped: 1 Per: 37
1 38 23 24 0 39 39 2 0 2 1 1 Ped: 1 Per: 38
1 39 23 24 0 0 0 1 0 2 1 1 Ped: 1 Per: 39
1 40 27 28 0 0 0 1 0 2 1 3 Ped: 1 Per: 40
.dat file
2 0 0 5 << NO. OF LOCI, RISK LOCUS, SEXLINKED (IF 1) PROGRAM
0 0.0 0.0 0 << MUT LOCUS, MUT MALE, MUT FEM, HAP FREQ (IF 1)
1 2
1 2 << AFFECTION, NO. OF ALLELES
0.9999 1.00000E-04 << GENE FREQUENCIES
1 << NO. OF LIABILITY CLASSES
0.0000 1.0000 1.0000 << PENETRANCES
3 4 << ALLELE NUMBERS, NO. OF ALLELES
0.6878 0.1667 0.0833 0.0625 << GENE FREQUENCIES
0 0 << SEX DIFFERENCE, INTERFERENCE (IF 1 OR 2)
0.10000 << RECOMBINATION VALUES
1 0.10000 0.45000 << REC VARIED, INCREMENT, FINISHING VALUE
CHEN-JEE HORNG, M.D.
DEPARTMENT OF PSYCHIATRY
VETERANS GENERAL HOSPITAL-TAIPEI
TAIPEI, TAIWAN, R.O.C.
E-MAIL: YMMCS023 at TWNMOE10.EDU.TW
FAX: 886-2-8742441
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