- 論文
- どんな解析ができる？(こちら)
- データのクオリティを含む基本記述統計
- アレル頻度とHardy-Weinberg 平衡検定
- 遺伝率の推定と家族内相関の計算
- 遺伝形式、浸透率を表す関数を、発症年齢による違いを含めて推定
- 血縁関係者におけるIBD推定
- パラメトリック連鎖解析
- ノンパラメトリック連鎖解析
- TDT解析
- 家系データにおけるアレルと形質の関連解析・非血縁標本に夜アレルと形質の関連解析
- ウェブサイト(opensage)
- まずは、動いてくれないとどうにもならないので、今、一番やりたい分離比解析が動くようにしてみる
- GUIは「親切そう」でいて、実は結構使いづらい…
- しかし、すべてのファイルをテキストエディタで作るのも結構面倒臭い
- なぜなら、いろいろな解析手法でパラメタファイルがわかりにくいから(そしてマニュアルが分かりにくいから、そしてサンプルファイルがいまいちだから…)
- 入力ファイルの原則は２つ
- 血縁関係と個人のフェノタイプ(とジェノタイプを書くファイル)
- 解析アプリの実行パラメタのファイル
- 分離比解析の例を取る
FAMILY IND FATHER MOTHER SEX AFFECTIOn AGE_EXAM AGE_ONSET
1 1 . . 0 1 60 50
1 2 . . 1 0 60 50
1 3 2 1 0 1 30 20
1 4 2 1 1 1 25 20
2 1 . . 0 1 60 50
2 2 . . 1 0 60 50
2 3 2 1 0 1 30 20
2 4 2 1 1 1 25 20
3 1 . . 0 1 60 50
3 2 . . 1 0 60 50
3 3 2 1 0 1 30 20
3 4 2 1 1 1 25 20
4 1 . . 0 1 60 50
4 2 . . 1 0 60 50
4 3 2 1 0 1 30 20
4 4 2 1 1 1 25 20
=====================================================================================================
SEGREG Analysis for Trait : AFFECTIOn
=====================================================================================================
# Model Specification
Model Class MLM
Type susceptibilities : one susceptibility
Residual correlations : No spouse correlation, parent-offspring and
sib-sib correlations equal
Type frequency :
Transmission : homogeneous no transmission
# Number of constituent pedigrees : 4
# Number of unconnected individuals : 0
# Final Estimates :
Parameter Parameter Est. Standard Err. First Deriv. Status
-----------------------------------------------------------------------------------------------------
susc 1.23132670 ----------- -0.15668816 Independent
marital resid a 0.00000000 ----------- Fixed
po = ss resid a -1.66901841 ----------- -0.59218639 Independent
-----------------------------------------------------------------------------------------------------
%SEGREG-I: The likelihood surface is flat and standard errors cannot be
computed.
Variance-covariance matrix not available due to computational problems.
See below.
-----------------------------------------------------------------------------------------------------
Residual Correlations
AA AB BB Overall
-----------------------------------------------------------------------------------------------------
father_mother 0.0000 0.0000 0.0000 0
father_offspring -0.2919 -0.2919 -0.2919 -0.291905
mother_offspring -0.2919 -0.2919 -0.2919 -0.291905
sib_sib -0.2919 -0.2919 -0.2919 -0.291905
-----------------------------------------------------------------------------------------------------
LN(Likelihood) : -7.88794
-2 LN(Likelihood) : 15.7759
Akaike's AIC score : 19.7759
=====================================================================================================
%SEGREG-E: Likelihood may not be maximized because of model constraints on
parameters.
%SEGREG-E: Estimating fewer parameters may help.
=====================================================================================================
SEGREG Analysis for Trait : AFFECTIOn
=====================================================================================================
# Model Specification
Model Class MLM
Type susceptibilities : two susceptibilities
Residual correlations : No spouse correlation, parent-offspring and
sib-sib correlations equal
Type frequency : Hardy-Weinberg equilibrium
Transmission : homogeneous no transmission
# Number of constituent pedigrees : 4
# Number of unconnected individuals : 0
# Final Estimates :
Parameter Parameter Est. Standard Err. First Deriv. Status
-----------------------------------------------------------------------------------------------------
susc_AA_AB 0.74945359 ----------- 0.00000000 Independent
susc_BB 1.19623294 ----------- 0.00653058 Independent
marital resid a 0.00000000 ----------- Fixed
po = ss resid a -1.69606585 ----------- -0.58576630 Independent
prob_AA 0.00000000 ----------- Dependent
prob_AB 0.00000000 ----------- Dependent
prob_BB 1.00000000 ----------- Dependent
freq_A 0.00000000 ----------- 0.00000000 Ind. func. fixed @ bnd
-----------------------------------------------------------------------------------------------------
%SEGREG-I: The likelihood surface is flat and standard errors cannot be
computed.
Variance-covariance matrix not available due to computational problems.
See below.
-----------------------------------------------------------------------------------------------------
Residual Correlations
AA AB BB Overall
-----------------------------------------------------------------------------------------------------
father_mother 0.0000 0.0000 0.0000 0
father_offspring -0.3696 -0.3696 -0.3023 -0.302331
mother_offspring -0.3696 -0.3696 -0.3023 -0.302331
sib_sib -0.3696 -0.3696 -0.3023 -0.302331
-----------------------------------------------------------------------------------------------------
LN(Likelihood) : -7.86935
-2 LN(Likelihood) : 15.7387
Akaike's AIC score : 21.7387
=====================================================================================================
%SEGREG-E: Likelihood may not be maximized because of model constraints on
parameters.
%SEGREG-E: Estimating fewer parameters may help.
=====================================================================================================
SEGREG Analysis for Trait : AFFECTIOn
=====================================================================================================
# Model Specification
Model Class MLM
Type susceptibilities : three susceptibilities
Residual correlations : No spouse correlation, parent-offspring and
sib-sib correlations equal
Type frequency : Hardy-Weinberg equilibrium
Transmission : homogeneous no transmission
# Number of constituent pedigrees : 4
# Number of unconnected individuals : 0
# Final Estimates :
Parameter Parameter Est. Standard Err. First Deriv. Status
-----------------------------------------------------------------------------------------------------
susc_AA 1.19474432 ----------- 0.00000000 Independent
susc_AB 1.19623294 ----------- 0.00000000 Independent
susc_BB 1.19623294 ----------- 0.00000000 Independent
marital resid a 0.00000000 ----------- Fixed
po = ss resid a -1.69606585 ----------- 0.00000000 Independent
prob_AA 0.00000000 ----------- Dependent
prob_AB 0.00001025 ----------- Dependent
prob_BB 0.99998975 ----------- Dependent
freq_A 0.00000513 ----------- 0.00000000 Independent functional
-----------------------------------------------------------------------------------------------------
%SEGREG-I: The likelihood surface is flat and standard errors cannot be
computed.
Variance-covariance matrix not available due to computational problems.
See below.
-----------------------------------------------------------------------------------------------------
Residual Correlations
AA AB BB Overall
-----------------------------------------------------------------------------------------------------
father_mother 0.0000 0.0000 0.0000 0
father_offspring -0.3026 -0.3023 -0.3023 -0.302331
mother_offspring -0.3026 -0.3023 -0.3023 -0.302331
sib_sib -0.3026 -0.3023 -0.3023 -0.302331
-----------------------------------------------------------------------------------------------------
LN(Likelihood) : -7.86935
-2 LN(Likelihood) : 15.7387
Akaike's AIC score : 25.7387
=====================================================================================================
==================================================================================
Likelihoods for Commingling Analysis
Option LN(Likelihood) -2 LN(Likelihood) Akaike's AIC score
----------------------------------------------------------------------------------
one susceptibility -7.8879 15.7759 19.7759
two susceptibilities -7.8694 15.7387 21.7387
three susceptibilities -7.8694 15.7387 25.7387
==================================================================================
- 実行コマンド
- 実行プログラムにパラメタファイル、データファイルの順で引き渡している
C:\S.A.G.E.v6.3\bin>segreg.exe C:\Users\ryamada\Desktop\SAGE\test2\SEGREG8.par C
:\Users\ryamada\Desktop\SAGE\test2\pedigree0.dat
=====================================================================================================
SEGREG Analysis for Trait : AFFECTIOn
=====================================================================================================
# Model Specification
Model Class MLM
Type susceptibilities : one susceptibility
Residual correlations : No spouse correlation, parent-offspring and
sib-sib correlations equal
Type frequency :
Transmission : homogeneous no transmission
# Number of constituent pedigrees : 4
# Number of unconnected individuals : 0
# Final Estimates :
Parameter Parameter Est. Standard Err. First Deriv. Status
-----------------------------------------------------------------------------------------------------
susc 1.23132670 ----------- -0.15668816 Independent
marital resid a 0.00000000 ----------- Fixed
po = ss resid a -1.66901841 ----------- -0.59218639 Independent
-----------------------------------------------------------------------------------------------------
%SEGREG-I: The likelihood surface is flat and standard errors cannot be
computed.
Variance-covariance matrix not available due to computational problems.
See below.
-----------------------------------------------------------------------------------------------------
Residual Correlations
AA AB BB Overall
-----------------------------------------------------------------------------------------------------
father_mother 0.0000 0.0000 0.0000 0
father_offspring -0.2919 -0.2919 -0.2919 -0.291905
mother_offspring -0.2919 -0.2919 -0.2919 -0.291905
sib_sib -0.2919 -0.2919 -0.2919 -0.291905
-----------------------------------------------------------------------------------------------------
LN(Likelihood) : -7.88794
-2 LN(Likelihood) : 15.7759
Akaike's AIC score : 19.7759
=====================================================================================================
%SEGREG-E: Likelihood may not be maximized because of model constraints on
parameters.
%SEGREG-E: Estimating fewer parameters may help.
=====================================================================================================
SEGREG Analysis for Trait : AFFECTIOn
=====================================================================================================
# Model Specification
Model Class MLM
Type susceptibilities : two susceptibilities
Residual correlations : No spouse correlation, parent-offspring and
sib-sib correlations equal
Type frequency : Hardy-Weinberg equilibrium
Transmission : homogeneous no transmission
# Number of constituent pedigrees : 4
# Number of unconnected individuals : 0
# Final Estimates :
Parameter Parameter Est. Standard Err. First Deriv. Status
-----------------------------------------------------------------------------------------------------
susc_AA_AB 0.74945359 ----------- 0.00000000 Independent
susc_BB 1.19623294 ----------- 0.00653058 Independent
marital resid a 0.00000000 ----------- Fixed
po = ss resid a -1.69606585 ----------- -0.58576630 Independent
prob_AA 0.00000000 ----------- Dependent
prob_AB 0.00000000 ----------- Dependent
prob_BB 1.00000000 ----------- Dependent
freq_A 0.00000000 ----------- 0.00000000 Ind. func. fixed @ bnd
-----------------------------------------------------------------------------------------------------
%SEGREG-I: The likelihood surface is flat and standard errors cannot be
computed.
Variance-covariance matrix not available due to computational problems.
See below.
-----------------------------------------------------------------------------------------------------
Residual Correlations
AA AB BB Overall
-----------------------------------------------------------------------------------------------------
father_mother 0.0000 0.0000 0.0000 0
father_offspring -0.3696 -0.3696 -0.3023 -0.302331
mother_offspring -0.3696 -0.3696 -0.3023 -0.302331
sib_sib -0.3696 -0.3696 -0.3023 -0.302331
-----------------------------------------------------------------------------------------------------
LN(Likelihood) : -7.86935
-2 LN(Likelihood) : 15.7387
Akaike's AIC score : 21.7387
=====================================================================================================
%SEGREG-E: Likelihood may not be maximized because of model constraints on
parameters.
%SEGREG-E: Estimating fewer parameters may help.
=====================================================================================================
SEGREG Analysis for Trait : AFFECTIOn
=====================================================================================================
# Model Specification
Model Class MLM
Type susceptibilities : three susceptibilities
Residual correlations : No spouse correlation, parent-offspring and
sib-sib correlations equal
Type frequency : Hardy-Weinberg equilibrium
Transmission : homogeneous no transmission
# Number of constituent pedigrees : 4
# Number of unconnected individuals : 0
# Final Estimates :
Parameter Parameter Est. Standard Err. First Deriv. Status
-----------------------------------------------------------------------------------------------------
susc_AA 1.19474432 ----------- 0.00000000 Independent
susc_AB 1.19623294 ----------- 0.00000000 Independent
susc_BB 1.19623294 ----------- 0.00000000 Independent
marital resid a 0.00000000 ----------- Fixed
po = ss resid a -1.69606585 ----------- 0.00000000 Independent
prob_AA 0.00000000 ----------- Dependent
prob_AB 0.00001025 ----------- Dependent
prob_BB 0.99998975 ----------- Dependent
freq_A 0.00000513 ----------- 0.00000000 Independent functional
-----------------------------------------------------------------------------------------------------
%SEGREG-I: The likelihood surface is flat and standard errors cannot be
computed.
Variance-covariance matrix not available due to computational problems.
See below.
-----------------------------------------------------------------------------------------------------
Residual Correlations
AA AB BB Overall
-----------------------------------------------------------------------------------------------------
father_mother 0.0000 0.0000 0.0000 0
father_offspring -0.3026 -0.3023 -0.3023 -0.302331
mother_offspring -0.3026 -0.3023 -0.3023 -0.302331
sib_sib -0.3026 -0.3023 -0.3023 -0.302331
-----------------------------------------------------------------------------------------------------
LN(Likelihood) : -7.86935
-2 LN(Likelihood) : 15.7387
Akaike's AIC score : 25.7387
=====================================================================================================
==================================================================================
Likelihoods for Commingling Analysis
Option LN(Likelihood) -2 LN(Likelihood) Akaike's AIC score
----------------------------------------------------------------------------------
one susceptibility -7.8879 15.7759 19.7759
two susceptibilities -7.8694 15.7387 21.7387
three susceptibilities -7.8694 15.7387 25.7387
==================================================================================
=====================================================================================================
SEGREG Analysis for Trait : AFFECTIOn
=====================================================================================================
# Model Specification
Model Class MLM
Type susceptibilities : one susceptibility
Residual correlations : No spouse correlation, parent-offspring and
sib-sib correlations equal
Type frequency :
Transmission : homogeneous no transmission
# Number of constituent pedigrees : 4
# Number of unconnected individuals : 0
# Final Estimates :
Parameter Parameter Est. Standard Err. First Deriv. Status
-----------------------------------------------------------------------------------------------------
susc 1.23132670 ----------- -0.15668816 Independent
marital resid a 0.00000000 ----------- Fixed
po = ss resid a -1.66901841 ----------- -0.59218639 Independent
-----------------------------------------------------------------------------------------------------
%SEGREG-I: The likelihood surface is flat and standard errors cannot be
computed.
-----------------------------------------------------------------------------------------------------
Residual Correlations
AA AB BB Overall
-----------------------------------------------------------------------------------------------------
father_mother 0.0000 0.0000 0.0000 0
father_offspring -0.2919 -0.2919 -0.2919 -0.291905
mother_offspring -0.2919 -0.2919 -0.2919 -0.291905
sib_sib -0.2919 -0.2919 -0.2919 -0.291905
-----------------------------------------------------------------------------------------------------
LN(Likelihood) : -7.88794
-2 LN(Likelihood) : 15.7759
Akaike's AIC score : 19.7759
=====================================================================================================
%SEGREG-E: Likelihood may not be maximized because of model constraints on
parameters.
%SEGREG-E: Estimating fewer parameters may help.
=====================================================================================================
SEGREG Analysis for Trait : AFFECTIOn
=====================================================================================================
# Model Specification
Model Class MLM
Type susceptibilities : two susceptibilities
Residual correlations : No spouse correlation, parent-offspring and
sib-sib correlations equal
Type frequency : Hardy-Weinberg equilibrium
Transmission : homogeneous no transmission
# Number of constituent pedigrees : 4
# Number of unconnected individuals : 0
# Final Estimates :
Parameter Parameter Est. Standard Err. First Deriv. Status
-----------------------------------------------------------------------------------------------------
susc_AA_AB 0.74945359 ----------- 0.00000000 Independent
susc_BB 1.19623294 ----------- 0.00653058 Independent
marital resid a 0.00000000 ----------- Fixed
po = ss resid a -1.69606585 ----------- -0.58576630 Independent
prob_AA 0.00000000 ----------- Dependent
prob_AB 0.00000000 ----------- Dependent
prob_BB 1.00000000 ----------- Dependent
freq_A 0.00000000 ----------- 0.00000000 Ind. func. fixed @ bnd
-----------------------------------------------------------------------------------------------------
%SEGREG-I: The likelihood surface is flat and standard errors cannot be
computed.
-----------------------------------------------------------------------------------------------------
Residual Correlations
AA AB BB Overall
-----------------------------------------------------------------------------------------------------
father_mother 0.0000 0.0000 0.0000 0
father_offspring -0.3696 -0.3696 -0.3023 -0.302331
mother_offspring -0.3696 -0.3696 -0.3023 -0.302331
sib_sib -0.3696 -0.3696 -0.3023 -0.302331
-----------------------------------------------------------------------------------------------------
LN(Likelihood) : -7.86935
-2 LN(Likelihood) : 15.7387
Akaike's AIC score : 21.7387
=====================================================================================================
%SEGREG-E: Likelihood may not be maximized because of model constraints on
parameters.
%SEGREG-E: Estimating fewer parameters may help.
=====================================================================================================
SEGREG Analysis for Trait : AFFECTIOn
=====================================================================================================
# Model Specification
Model Class MLM
Type susceptibilities : three susceptibilities
Residual correlations : No spouse correlation, parent-offspring and
sib-sib correlations equal
Type frequency : Hardy-Weinberg equilibrium
Transmission : homogeneous no transmission
# Number of constituent pedigrees : 4
# Number of unconnected individuals : 0
# Final Estimates :
Parameter Parameter Est. Standard Err. First Deriv. Status
-----------------------------------------------------------------------------------------------------
susc_AA 1.19474432 ----------- 0.00000000 Independent
susc_AB 1.19623294 ----------- 0.00000000 Independent
susc_BB 1.19623294 ----------- 0.00000000 Independent
marital resid a 0.00000000 ----------- Fixed
po = ss resid a -1.69606585 ----------- 0.00000000 Independent
prob_AA 0.00000000 ----------- Dependent
prob_AB 0.00001025 ----------- Dependent
prob_BB 0.99998975 ----------- Dependent
freq_A 0.00000513 ----------- 0.00000000 Independent functional
-----------------------------------------------------------------------------------------------------
%SEGREG-I: The likelihood surface is flat and standard errors cannot be
computed.
-----------------------------------------------------------------------------------------------------
Residual Correlations
AA AB BB Overall
-----------------------------------------------------------------------------------------------------
father_mother 0.0000 0.0000 0.0000 0
father_offspring -0.3026 -0.3023 -0.3023 -0.302331
mother_offspring -0.3026 -0.3023 -0.3023 -0.302331
sib_sib -0.3026 -0.3023 -0.3023 -0.302331
-----------------------------------------------------------------------------------------------------
LN(Likelihood) : -7.86935
-2 LN(Likelihood) : 15.7387
Akaike's AIC score : 25.7387
=====================================================================================================
