Resultats des analyses biq¶
Cas General / Résultats demi-freres (ndmin=50)¶
- jeux de données porcqtl
Quasi-newton¶
Solution avec le point initial :
par(dg%np+1)=1000d0 !// P1 par(dg%np+2)=1000d0 !// P2 par(dg%np+3)=1000d0 !// P3 par(2*dg%np+3+dataw%ndamestim+1)=0.d0 !//Alpha1 par(2*dg%np+3+dataw%ndamestim+2)=0.d0 !//Alpha2 par(2*dg%np+3+dataw%ndamestim+3)=0.d0 !//Alpha3 par(2*dg%np+3+dataw%ndamestim+4)=0.d0 !//Alpha4
Le quasi-newton rend pratiquement à tous les point une erreur :
qtlmap:[14/02/2013 11:00:04][warning]:NLOPT_FAILURE WARNING:NLOPT_FAILURE
** chromosome 7 **
I-----------I-----------I-----------I-----------I
30.9 - oo
29.6 I o o o
28.4 I o o
27.1 I o
25.8 I o
24.5 I
23.2 - o
21.9 I o
20.6 I
19.3 I o
18.0 I
16.8 I o
15.5 - o
14.2 I
12.9 I o
11.6 I o o oo o oo o oo o
10.3 I oo o
9.0 I
7.7 -
6.4 I
5.2 I
3.9 I
2.6 I
1.3 I
0.0 - o
I-----------I-----------I-----------I-----------I
0.21 0.57 0.93 1.30 1.66
Maximum likelihood ratio test :
Test H0 / H1 : 30.93169
The maximum is reached at position(s) 0.5600(Chr :7 )
flanking marker (qtl: 1) ,SW1369 ,SLA
---------------------------------------------------------------
Estimation of parameters under H1
---------------------------------------------------------------
Within sire standard deviation
sire 910001 s.d. : 0.517
sire 910045 s.d. : 0.467
sire 910081 s.d. : 0.636
sire 910088 s.d. : 0.617
parameter estimable ? value precision
Qtl effect
QQ [prob=0%] yes -1.538 0.000
Qq [prob=5%] yes -2.270 0.000
qQ [prob=0%] yes -1.929 0.000
qq [prob=94%] yes -2.483 0.000
Mean Sire
Sire 910001 yes 238.747 0.000
Sire 910045 yes 8.598 0.000
Sire 910081 yes 9.045 0.000
Sire 910088 yes 8.946 0.000
Simplex¶
--------------------------
*****
** chromosome 7 **
I-----------I-----------I-----------I-----------I
30.5 - o
29.5 I o o o
28.5 I o o
27.6 I o
26.6 I o
25.6 I
24.7 - o
23.7 I
22.7 I o
21.8 I o
20.8 I
19.8 I
18.9 - o o
17.9 I
17.0 I
16.0 I o o
15.0 I
14.1 I o
13.1 - o
12.1 I o o oo
11.2 I ooo o oo oo
10.2 I o oo
9.2 I o
8.3 I
7.3 - o
I-----------I-----------I-----------I-----------I
0.01 0.42 0.83 1.25 1.66
Maximum likelihood ratio test :
Test H0 / H1 : 30.46298
The maximum is reached at position(s) 0.5600(Chr :7 )
flanking marker (qtl: 1) ,SW1369 ,SLA
---------------------------------------------------------------
Estimation of parameters under H1
---------------------------------------------------------------
Within sire standard deviation
sire 910001 s.d. : 0.522
sire 910045 s.d. : 0.469
sire 910081 s.d. : 0.635
sire 910088 s.d. : 0.624
parameter estimable ? value precision
Qtl effect
QQ [prob=4%] yes 22.462 0.000
Qq [prob=4%] yes 21.899 0.000
qQ [prob=0%] yes 22.853 0.000
qq [prob=90%] yes 22.124 0.000
Mean Sire
Sire 910001 yes 1255.563 0.000
Sire 910045 yes -15.792 0.000
Sire 910081 yes -15.336 0.000
Sire 910088 yes -15.444 0.000
sbplex¶
I-----------I-----------I-----------I-----------I
30.9 - o
30.1 I o o o
29.2 I o o
28.4 I o
27.5 I o
26.7 I
25.8 -
25.0 I o
24.1 I o
23.2 I
22.4 I o
21.5 I
20.7 - o
19.8 I
19.0 I o o o
18.1 I o
17.3 I
16.4 I o o
15.6 - o
14.7 I
13.8 I
13.0 I o
12.1 I o o
11.3 I o ooo o o oo oo
10.4 - oo
I-----------I-----------I-----------I-----------I
0.01 0.42 0.83 1.25 1.66
Maximum likelihood ratio test :
Test H0 / H1 : 30.93175
The maximum is reached at position(s) 0.5600(Chr :7 )
flanking marker (qtl: 1) ,SW1369 ,SLA
---------------------------------------------------------------
Estimation of parameters under H1
---------------------------------------------------------------
Within sire standard deviation
sire 910001 s.d. : 0.517
sire 910045 s.d. : 0.467
sire 910081 s.d. : 0.636
sire 910088 s.d. : 0.617
parameter estimable ? value precision
Qtl effect
QQ [prob=0%] yes 0.198 0.000
Qq [prob=94%] yes -0.534 0.000
qQ [prob=5%] yes -0.193 0.000
qq [prob=0%] yes -0.747 0.000
Mean Sire
Sire 910001 yes 2766.851 0.000
Sire 910045 yes 6.862 0.000
Sire 910081 yes 7.308 0.000
Sire 910088 yes 7.210 0.000
Cas General / Resultat plein frere (ndmin=15)¶
Quasi-newton¶
The mean of absolute value of substitution effect WQ (in std unit) =
--------------------------
--------------------------
*****
** chromosome 7 **
I-----------I-----------I-----------I-----------I
51.8 - o
49.7 I
47.5 I o o
45.4 I
43.2 I o o
41.0 I
38.9 - o
36.7 I
34.6 I o o o
32.4 I o
30.2 I
28.1 I o
25.9 - o
23.8 I
21.6 I o o oo oo o
19.4 I o o
17.3 I
15.1 I o o
13.0 - o oo
10.8 I o
8.6 I o
6.5 I
4.3 I
2.2 I
0.0 - o o
I-----------I-----------I-----------I-----------I
0.01 0.42 0.83 1.25 1.66
Maximum likelihood ratio test :
Test H0 / H1 : 51.83860
The maximum is reached at position(s) 0.6600(Chr :7 )
flanking marker (qtl: 1) ,SLA ,S0102
---------------------------------------------------------------
Estimation of parameters under H1
---------------------------------------------------------------
Within sire standard deviation
sire 910001 s.d. : 0.494
sire 910045 s.d. : 0.505
sire 910081 s.d. : 0.570
sire 910088 s.d. : 0.574
parameter estimable ? value precision
Qtl effect
QQ [prob=0%] yes 1.438 0.000
Qq [prob=7%] yes 0.798 0.000
qQ [prob=0%] yes 0.966 0.000
qq [prob=92%] yes 0.639 0.000
Mean Sire
Sire 910001 yes 73.958 0.000
Sire 910045 yes 5.693 0.000
Sire 910081 yes 6.029 0.000
Sire 910088 yes 6.194 0.000
Mean dam
Dam 910014 [Sire 910001] yes -0.963 0.000
Dam 910071 [Sire 910001] yes 0.185 0.000
Dam 910002 [Sire 910081] yes 0.245 0.000
Dam 910010 [Sire 910081] yes -0.052 0.000
Dam 910009 [Sire 910088] yes -0.128 0.000
Dam 910069 [Sire 910088] yes 0.213 0.000
Dam 910074 [Sire 910088] yes 0.390 0.000
Simplexe¶
The mean of absolute value of substitution effect WQ (in std unit) =
--------------------------
--------------------------
*****
** chromosome 7 **
I-----------I-----------I-----------I-----------I
56.3 - o
54.3 I
52.2 I o o
50.2 I
48.1 I
46.1 I o o
44.0 - o
42.0 I
40.0 I
37.9 I o
35.9 I o o
33.8 I o
31.8 - o
29.7 I
27.7 I o
25.7 I o
23.6 I o oo o
21.6 I o o
19.5 - o oo o
17.5 I o
15.5 I o o
13.4 I o
11.4 I o o o
9.3 I o o
7.3 - o o
I-----------I-----------I-----------I-----------I
0.01 0.42 0.83 1.25 1.66
Maximum likelihood ratio test :
Test H0 / H1 : 56.29237
The maximum is reached at position(s) 0.6600(Chr :7 )
flanking marker (qtl: 1) ,SLA ,S0102
---------------------------------------------------------------
Estimation of parameters under H1
---------------------------------------------------------------
Within sire standard deviation
sire 910001 s.d. : 0.491
sire 910045 s.d. : 0.512
sire 910081 s.d. : 0.589
sire 910088 s.d. : 0.586
parameter estimable ? value precision
Qtl effect
QQ [prob=1%] yes -89.091 0.000
Qq [prob=6%] yes -89.805 0.000
qQ [prob=0%] yes -89.560 0.000
qq [prob=92%] yes -89.955 0.000
Mean Sire
Sire 910001 yes 4417.157 0.000
Sire 910045 yes 96.017 0.000
Sire 910081 yes 96.575 0.000
Sire 910088 yes 96.619 0.000
Mean dam
Dam 910014 [Sire 910001] yes 58.642 0.000
Dam 910071 [Sire 910001] yes 0.476 0.000
Dam 910002 [Sire 910081] yes 0.569 0.000
Dam 910010 [Sire 910081] yes 0.136 0.000
Dam 910009 [Sire 910088] yes 0.042 0.000
Dam 910069 [Sire 910088] yes 31.158 0.000
Dam 910074 [Sire 910088] yes 31.352 0.000
Sbplx¶
I-----------I-----------I-----------I-----------I
54.5 - o
52.6 I
50.6 I o
48.7 I o
46.8 I
44.9 I
43.0 - o
41.1 I o o
39.1 I
37.2 I
35.3 I o
33.4 I
31.5 - o o
29.6 I o
27.6 I o
25.7 I
23.8 I o
21.9 I
20.0 - o
18.1 I o
16.1 I ooo oo oo
14.2 I o
12.3 I o o o o o
10.4 I oo oo o o
8.5 - o
I-----------I-----------I-----------I-----------I
0.01 0.42 0.83 1.25 1.66
Maximum likelihood ratio test :
Test H0 / H1 : 54.48156
The maximum is reached at position(s) 0.6600(Chr :7 )
flanking marker (qtl: 1) ,SLA ,S0102
---------------------------------------------------------------
Estimation of parameters under H1
---------------------------------------------------------------
Within sire standard deviation
sire 910001 s.d. : 0.478
sire 910045 s.d. : 0.565
sire 910081 s.d. : 0.570
sire 910088 s.d. : 0.564
parameter estimable ? value precision
Qtl effect
QQ [prob=0%] yes -0.225 0.000
Qq [prob=99%] yes 0.090 0.000
qQ [prob=0%] yes 0.032 0.000
qq [prob=0%] yes 0.763 0.000
Mean Sire
Sire 910001 yes 7.169 0.000
Sire 910045 yes 6.813 0.000
Sire 910081 yes 7.200 0.000
Sire 910088 yes 7.376 0.000
Mean dam
Dam 910014 [Sire 910001] yes 0.102 0.000
Dam 910071 [Sire 910001] yes -0.096 0.000
Dam 910002 [Sire 910081] yes 0.009 0.000
Dam 910010 [Sire 910081] yes -0.406 0.000
Dam 910009 [Sire 910088] yes -0.470 0.000
Dam 910069 [Sire 910088] yes -0.033 0.000
Dam 910074 [Sire 910088] yes 0.194 0.000
Cas Additif / Resultat demi frere (ndmin=50)¶
Quasi newton
I-----------I-----------I-----------I-----------I
29.0 - o o
27.8 I oo o
26.6 I o o
25.4 I
24.2 I o
23.0 I
21.8 -
20.6 I o
19.3 I
18.1 I
16.9 I
15.7 I o
14.5 -
13.3 I
12.1 I o
10.9 I
9.7 I
8.5 I
7.3 - o
6.0 I
4.8 I oo o oo
3.6 I o o oo o oo o o
2.4 I
1.2 I
0.0 - o o
I-----------I-----------I-----------I-----------I
0.21 0.57 0.93 1.30 1.66
Maximum likelihood ratio test :
Test H0 / H1 : 29.02490
The maximum is reached at position(s) 0.5600(Chr :7 )
flanking marker (qtl: 1) ,SW1369 ,SLA
---------------------------------------------------------------
Estimation of parameters under H1
---------------------------------------------------------------
Within sire standard deviation
sire 910001 s.d. : 0.517
sire 910045 s.d. : 0.480
sire 910081 s.d. : 0.637
sire 910088 s.d. : 0.616
parameter estimable ? value precision
Qtl effect
QQ [prob=0%] yes -0.705 0.000
Qq [prob=94%] yes -1.136 0.000
qQ [prob=5%] yes -1.136 0.000
qq [prob=0%] yes -1.566 0.000
Mean Sire
Sire 910001 yes 79.555 0.000
Sire 910045 yes 7.785 0.000
Sire 910081 yes 8.172 0.000
Sire 910088 yes 8.134 0.000
Simplex¶
I-----------I-----------I-----------I-----------I
28.7 - o o
27.6 I o o
26.5 I o o o
25.4 I
24.2 I o
23.1 I o
22.0 -
20.9 I
19.7 I o o
18.6 I
17.5 I
16.4 I o
15.2 - o
14.1 I
13.0 I
11.9 I o o o
10.7 I
9.6 I
8.5 - o
7.4 I o
6.2 I
5.1 I oo
4.0 I o ooo oo o o oo
2.9 I o o o
1.7 - o
I-----------I-----------I-----------I-----------I
0.01 0.42 0.83 1.25 1.66
Maximum likelihood ratio test :
Test H0 / H1 : 28.74529
The maximum is reached at position(s) 0.5600(Chr :7 )
flanking marker (qtl: 1) ,SW1369 ,SLA
---------------------------------------------------------------
Estimation of parameters under H1
---------------------------------------------------------------
Within sire standard deviation
sire 910001 s.d. : 0.517
sire 910045 s.d. : 0.476
sire 910081 s.d. : 0.640
sire 910088 s.d. : 0.625
parameter estimable ? value precision
Qtl effect
QQ [prob=2%] yes 59.122 0.000
Qq [prob=91%] yes 58.691 0.000
qQ [prob=5%] yes 58.691 0.000
qq [prob=0%] yes 58.261 0.000
Mean Sire
Sire 910001 yes 1495.113 0.000
Sire 910045 yes -52.043 0.000
Sire 910081 yes -51.655 0.000
Sire 910088 yes -51.694 0.000
Sbplex¶
I-----------I-----------I-----------I-----------I
29.0 - o
27.9 I o o o
26.9 I o o o
25.8 I
24.7 I o
23.6 I o
22.5 -
21.4 I
20.4 I o o
19.3 I
18.2 I
17.1 I
16.0 - o
15.0 I o
13.9 I
12.8 I oo
11.7 I o o
10.6 I
9.5 -
8.5 I
7.4 I
6.3 I o
5.2 I o o
4.1 I o o oo o o oo o
3.0 - o oo
I-----------I-----------I-----------I-----------I
0.11 0.50 0.88 1.27 1.66
Maximum likelihood ratio test :
Test H0 / H1 : 29.02490
The maximum is reached at position(s) 0.5600(Chr :7 )
flanking marker (qtl: 1) ,SW1369 ,SLA
---------------------------------------------------------------
Estimation of parameters under H1
---------------------------------------------------------------
Within sire standard deviation
sire 910001 s.d. : 0.517
sire 910045 s.d. : 0.480
sire 910081 s.d. : 0.637
sire 910088 s.d. : 0.616
parameter estimable ? value precision
Qtl effect
QQ [prob=0%] yes 0.038 0.000
Qq [prob=94%] yes -0.392 0.000
qQ [prob=5%] yes -0.392 0.000
qq [prob=0%] yes -0.823 0.000
Mean Sire
Sire 910001 yes 3961.087 0.000
Sire 910045 yes 7.041 0.000
Sire 910081 yes 7.428 0.000
Sire 910088 yes 7.390 0.000
Cas Additif / Resultat plein frere (ndmin=15)¶
Quasi-newton¶
*****
** chromosome 7 **
I-----------I-----------I-----------I-----------I
47.7 - o
45.9 I
44.2 I o o
42.5 I
40.7 I o
39.0 I o
37.3 -
35.5 I o
33.8 I
32.1 I o o
30.3 I o o
28.6 I
26.9 -
25.1 I
23.4 I o
21.6 I
19.9 I
18.2 I
16.4 - o
14.7 I o o
13.0 I o o o o
11.2 I o o
9.5 I o o o o
7.8 I o
6.0 - o
I-----------I-----------I-----------I-----------I
0.41 0.72 1.03 1.35 1.66
Maximum likelihood ratio test :
Test H0 / H1 : 47.66765
The maximum is reached at position(s) 0.6600(Chr :7 )
flanking marker (qtl: 1) ,SLA ,S0102
---------------------------------------------------------------
Estimation of parameters under H1
---------------------------------------------------------------
Within sire standard deviation
sire 910001 s.d. : 0.486
sire 910045 s.d. : 0.503
sire 910081 s.d. : 0.587
sire 910088 s.d. : 0.580
parameter estimable ? value precision
Qtl effect
QQ [prob=0%] yes 16.738 0.000
Qq [prob=92%] yes 16.315 0.000
qQ [prob=7%] yes 16.315 0.000
qq [prob=0%] yes 15.892 0.000
Mean Sire
Sire 910001 yes 116.677 0.000
Sire 910045 yes -9.655 0.000
Sire 910081 yes -9.308 0.000
Sire 910088 yes -9.147 0.000
Mean dam
Dam 910014 [Sire 910001] yes -16.322 0.000
Dam 910071 [Sire 910001] yes 0.185 0.000
Dam 910002 [Sire 910081] yes 0.245 0.000
Dam 910010 [Sire 910081] yes -0.052 0.000
Dam 910009 [Sire 910088] yes -0.128 0.000
Dam 910069 [Sire 910088] yes 0.213 0.000
Dam 910074 [Sire 910088] yes 0.390 0.000
NOTE: known allelic origin means QTL effect = maternal - paternal allele effects
Simplex¶
** chromosome 7 **
I-----------I-----------I-----------I-----------I
50.9 - o
49.1 I
47.2 I o o
45.4 I
43.5 I
41.7 I o o
39.9 -
38.0 I o
36.2 I
34.3 I o o
32.5 I o
30.7 I o
28.8 -
27.0 I o
25.1 I o
23.3 I
21.5 I o
19.6 I
17.8 - o
15.9 I o o oo
14.1 I oo o o
12.3 I oo o o
10.4 I o o oo
8.6 I o o
6.8 - o o
I-----------I-----------I-----------I-----------I
0.01 0.42 0.83 1.25 1.66
Maximum likelihood ratio test :
Test H0 / H1 : 50.89492
The maximum is reached at position(s) 0.6600(Chr :7 )
flanking marker (qtl: 1) ,SLA ,S0102
---------------------------------------------------------------
Estimation of parameters under H1
---------------------------------------------------------------
Within sire standard deviation
sire 910001 s.d. : 0.478
sire 910045 s.d. : 0.495
sire 910081 s.d. : 0.580
sire 910088 s.d. : 0.592
parameter estimable ? value precision
Qtl effect
QQ [prob=1%] yes -54.827 0.000
Qq [prob=93%] yes -55.275 0.000
qQ [prob=5%] yes -55.275 0.000
qq [prob=0%] yes -55.722 0.000
Mean Sire
Sire 910001 yes 2362.050 0.000
Sire 910045 yes 61.747 0.000
Sire 910081 yes 62.278 0.000
Sire 910088 yes 62.345 0.000
Mean dam
Dam 910014 [Sire 910001] yes -77.701 0.000
Dam 910071 [Sire 910001] yes 0.421 0.000
Dam 910002 [Sire 910081] yes 0.493 0.000
Dam 910010 [Sire 910081] yes 0.072 0.000
Dam 910009 [Sire 910088] yes 0.020 0.000
Dam 910069 [Sire 910088] yes 133.151 0.000
Dam 910074 [Sire 910088] yes 133.355 0.000
Sbplx variant of Nelder-Mead¶
** chromosome 7 **
I-----------I-----------I-----------I-----------I
47.3 - o
45.6 I o
43.9 I o
42.1 I
40.4 I o
38.7 I
37.0 - o o
35.2 I
33.5 I
31.8 I
30.0 I o o
28.3 I o
26.6 - o
24.9 I
23.1 I o
21.4 I o
19.7 I
18.0 I
16.2 - o o
14.5 I
12.8 I o oo
11.0 I o ooo o o
9.3 I oo oo o o o oo
7.6 I o
5.9 - o
I-----------I-----------I-----------I-----------I
0.01 0.42 0.83 1.25 1.66
Maximum likelihood ratio test :
Test H0 / H1 : 47.32789
The maximum is reached at position(s) 0.6600(Chr :7 )
flanking marker (qtl: 1) ,SLA ,S0102
---------------------------------------------------------------
Estimation of parameters under H1
---------------------------------------------------------------
Within sire standard deviation
sire 910001 s.d. : 0.475
sire 910045 s.d. : 0.574
sire 910081 s.d. : 0.582
sire 910088 s.d. : 0.580
parameter estimable ? value precision
Qtl effect
QQ [prob=0%] yes -0.306 0.000
Qq [prob=99%] yes 0.143 0.000
qQ [prob=0%] yes 0.143 0.000
qq [prob=0%] yes 0.592 0.000
Mean Sire
Sire 910001 yes 7.169 0.000
Sire 910045 yes 6.775 0.000
Sire 910081 yes 7.172 0.000
Sire 910088 yes 7.366 0.000
Mean dam
Dam 910014 [Sire 910001] yes 0.112 0.000
Dam 910071 [Sire 910001] yes -0.024 0.000
Dam 910002 [Sire 910081] yes 0.066 0.000
Dam 910010 [Sire 910081] yes -0.365 0.000
Dam 910009 [Sire 910088] yes -0.399 0.000
Dam 910069 [Sire 910088] yes 0.020 0.000
Dam 910074 [Sire 910088] yes 0.234 0.000