Développement du modèle de farnir¶
Vraisemblance¶
__
V = || V
i i
genotype du pere i, G(i) in { QQ,Qq,qQ,qq }
genotype de la mere i,i, G(i,j) in { QQ,Qq,qQ,qq }
prob(G(i)) in { P'1, P'2, P'3, P'4}
a
P'1 = ---------
1 + Sum (a+b+c)
b
P'2 = ---------
1 + Sum (a+b+c)
c
P'3 = ---------
1 + Sum (a+b+c)
1
P'4 = ---------
1 + Sum (a+b+c)
__ __
V = Sum [ prob(G(i)) * || Sum(G(i,j)) [ Sum [p(hd(ij)) || prob(G(i,j,k))]]]
i G(i) (i,j) nd
pour chaque position à tester :
prob(G(i,j,k)) = exp 1/2( Y(i,j,k) - Mu(i) - Mu(i,j) - [ pdd(1)* A[G(i)[1],G(i,j)[1]] + pdd(2)* A[G(i)[1],G(i,j)[2]] - pdd(3)* A[G(i)[2],G(i,j)[1]] - pdd(4)* A[G(i)[2],G(i,j)[2]]] )
Source¶
source:trunk/src/analyse/m_qtlmap_analyse_biallelic_farnir.f95
Note :
Pour modifier le modèle selon le tableau suivant :
| Général | Dominance | Additif |
| L1 | L1 | L1 |
| L2 | L2 | (L1+L2)/2 |
| L3 | L2 | (L1+L2)/2 |
| L4 | L3 | L2 |
Il faut décommenter les lignes ici : source:trunk/src/analyse/m_qtlmap_analyse_biallelic_farnir.f95#L320
Execution dans QTLMap¶
--calcul=40
Paramètres à estimer¶
P1 :
Summary des resultats Demi-Freres(ndmin=15)¶
Reference¶
calcul=1
I-----------I-----------I-----------I-----------I
53.2 - oo
51.3 I
49.4 I oo
47.5 I o
45.6 I
43.7 I o
41.8 -
40.0 I o
38.1 I
36.2 I o
34.3 I o
32.4 I o
30.5 - o
28.6 I
26.7 I o
24.8 I o o
22.9 I o o oo o
21.1 I o
19.2 - o o o
17.3 I o
15.4 I o o
13.5 I o o o
11.6 I o o o
9.7 I o
7.8 - o
I-----------I-----------I-----------I-----------I
0.01 0.42 0.83 1.25 1.66
Maximum likelihood ratio test :
Test H0 / H1 : 53.19069
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. : 0.484
sire 910045 s.d. : 0.567
sire 910081 s.d. : 0.578
sire 910088 s.d. : 0.568
parameter estimable ? value precision
Sire Qtl effect
Sire 910001 yes -0.178 0.000
Sire 910045 yes -0.121 0.000
Sire 910081 yes -0.203 0.000
Sire 910088 yes -0.255 0.000
Dam Qtl effect
Dam 910014 yes -0.287 0.000
Dam 910071 yes -0.219 0.000
Dam 910002 yes -0.450 0.000
Dam 910010 yes -0.186 0.000
Dam 910009 yes -0.134 0.000
Dam 910069 yes -0.084 0.000
Dam 910074 yes -0.337 0.000
Mean Sire
Sire 910001 yes 6.872 0.000
Sire 910045 yes 7.086 0.000
Sire 910081 yes 7.179 0.000
Sire 910088 yes 7.405 0.000
Mean dam
Dam 910014 [Sire 910001] yes -0.022 0.000
Dam 910071 [Sire 910001] yes 0.022 0.000
Dam 910002 [Sire 910081] yes 0.014 0.000
Dam 910010 [Sire 910081] yes -0.014 0.000
Dam 910009 [Sire 910088] yes -0.021 0.000
Dam 910069 [Sire 910088] yes 0.196 0.000
Dam 910074 [Sire 910088] yes -0.174 0.000
Additif¶
| Methode d'optim | MaxLRT | Pos | Prob(QQ) | Prob(Qq) | Prob(qQ) | Prob(qq) | ||||
| quasinewton | 47.66 | 0.66 | 0% | 16.738 | 92% | 16.315 | 7% | 15.892 | 0% | 15.892 |
| simplex | 50.89 | 0.66 | 1% | -54.827 | 93% | -55.275 | 5% | -55.275 | 0% | -55.722 |
| sbplx | 47.32 | 0.66 | 0% | -0.306 | 99% | 0.143 | 0% | 0.143 | 0% | 0.592 |
h3.
Additif ndmin=50¶
| Methode d'optim | MaxLRT | Pos | Prob(QQ) | Prob(Qq) | Prob(qQ) | Prob(qq) | ||||
| quasinewton | 29.02 | 0.56 | 0% | -0.705 | 94% | -1.136 | 5% | -1.136 | 0% | -1.566 |
| simplex | 28.74 | 0.56 | 2% | 59.122 | 91% | 58.691 | 5% | 58.691 | 0% | 58.261 |
| sbplx | 47.32 | 0.66 | 0% | 0.038 | 94% | -0.392 | 5% | -0.392 | 0% | -0.823 |
General ndmin=15¶
| Methode d'optim | MaxLRT | Pos | Prob(QQ) | Prob(Qq) | Prob(qQ) | Prob(qq) | ||||
| quasinewton | 51.83 | 0.66 | 0% | 1.438 | 92% | 0.798 | 7% | 0.966 | 0% | 0.639 |
| simplex | 56.29 | 0.66 | 1% | -89.091 | 92% | -89.805 | 6% | -89.560 | 0% | -89.955 |
| sbplx | 54.48 | 0.66 | 0% | -0.225 | 99% | 0.090 | 0% | 0.032 | 0% | 0.763 |
General ndmin=50¶
| Methode d'optim | MaxLRT | Pos | Prob(QQ) | Prob(Qq) | Prob(qQ) | Prob(qq) | ||||
| quasinewton | 30.93 | 0.56 | 0% | -1.538 | 94% | -2.270 | 5% | -1.929 | 0% | -2.483 |
| simplex | 30.62 | 0.56 | 3% | -16.301 | 91% | -17.034 | 5% | -16.692 | 0% | -17.246 |
| sbplx | 30.93 | 0.56 | 0% | 0.198 | 94% | -0.534 | 5% | -0.193 | 0% | -0.747 |