WOMBAT을 이용하여 Maternal Trait Model 풀기

WOMBAT을 이용하여 Maternal Trait Model 풀기

 

예제 자료

 

R.A. Mrode, Linear Models for the Prediction of Animal Breeding Values. 2nd. Edition

 

Page 123. Example 6.1

 

자료입력

 

5 2 2 1 1 35

6 2 2 1 2 20

7 6 6 1 2 25

8 5 5 1 1 40

9 6 6 2 1 42

10 2 2 2 2 22

11 7 7 2 2 35

12 7 7 3 2 34

13 2 2 3 1 20

14 6 6 3 2 40

 

개체, 어미, 어미, Herd, sex, 생시체중

 

위 자료를 data.txt로 저장

 

혈통입력

 

1 0 0

2 0 0

3 0 0

4 0 0

5 1 2

6 3 2

7 4 6

8 3 5

9 1 6

10 3 2

11 3 7

12 8 7

13 9 2

14 3 6

 

개체, 아비, 어미

 

위 자료를 pedi.txt로 저장

 

파라미터 파일 작성

 

# run option - 육종가를 구할 때

# RnSoln_xxx.dat 출력 파일 확인

#RUNOP -v --solvit

 

# run option - 육종가와 SEP(standard error of prediction)

# reliability(r2) = 1- SEP^2 / sigma_a^2

# RnSoln_xxx.dat 출력 파일 확인

RUNOP -v --blup

 

# run option - 좋은 초기값으로 분산성분을 추정할 때,

#RUNOP -v --good

 

# run option - 나쁜 초기값일 때 분산성분을 추정할 때,

#RUNOP -v --bad

 

# 요약 출력파일에 출력할 내용

COMMENT Single Trait Model(with Maternal Effects) from Mrode, 2nd Edition, Example 6.1

 

# Analysis Type, 단형질 분석

ANALYSIS UNI 1

 

# 혈통 파일 이름

# SumPedigree.out 확인

PED pedi.txt

 

# 자료 파일 이름

DATA data.txt

animal

gmdam 999

pedam 999

herd 3

sex 2

b_wt

END DATA

 

# Model of analysis

# SumModel.out 확인

MODEL

TR b_wt

FIX herd

FIX sex

RAN animal NRM

RAN gmdam NRM

RAN pedam IDE

END MODEL

 

 

# 분산 성분

VAR animal+gmdam 2

150 -40 90

 

VAR pedam 1

40

 

VAR error 1

350

 

# SumModel.out 확인

# SumEstimates.out 확인

# SumPedigree.out 확인

# FixSolutions.out 확인

# RnSoln_xxx.dat 확인

 

위 파라미터 파일을 wombat.par로 저장

 

실행

 

위 세 파일을 한 폴더에 넣고 다음과 같이 실행

 

 

 

 

 

결과 확인

 

SumModel.out

 

======= Version 19-05-2012 ======================================= **KM** ====

 

Program WOMBAT : Summary of information from Set-up step

==============================================================================

 

Single Trait Model(with Maternal Effects) from Mrode, 2nd Edition, Example

 

Analysis type : "UNI 1"

Data file : "data.txt"

Pedigree file : "pedi.txt"

Parameter file : "wombat.par"

 

 

No. of traits = 1

nrec mean sdev min. max.

1 "b_wt" 10 31.3000 8.70568 20.0000 42.0000

 

Fixed effects

1 "b_wt" nlev

1 "herd" 3

2 "sex" 2

 

Random effects nlev

1 "animal+gmdam 14 NRM

2 "pedam" 4 IDE

======== end of file ============================13-03-2014==========01:13====

 

SumPedigree.out

 

======= Version 19-05-2012 ======================================= **KM** ====

 

Program WOMBAT : Summary of Pedigree Information

==============================================================================

 

Single Trait Model(with Maternal Effects) from Mrode, 2nd Edition, Example

 

Analysis type : "UNI 1"

Data file : "data.txt"

Pedigree file : "pedi.txt"

Parameter file : "wombat.par"

 

 

No. of animal IDs in data file = = 11

No. of animal IDs in total = = 14

 

*****Pedigree Structure for random effect : 1 ****************************

Original no. of animals = 14

No. of animals after pruning = 14

... proportion (%) remaining = 100.0

 

No. of levels w/out records = 4

No. of levels with records = 10 100.0%

... 1 record(s) = 10 100.0%

No. of animals w/out offspring = 5 35.7%

No. of animals with offspring = 9 64.3%

... and records = 5 35.7%

No. of animals with unknown sire = 4

No. of animals with unknown dam = 4

No. of animals with both parents unknown = 4

No. of animals with records =

... and unknown sire = 0

... and unknown dam = 0

... and both parents unknown = 0

No. of sires = 5

... with progeny in the data = 5

... with records & progeny in data = 2

No. of dams = 4

... with progeny in the data = 4

... with records & progeny in data = 3

 

No. of animals with known/unpruned grand-parents

... with paternal grandsire = 2

... with paternal granddam = 2

... with maternal grandsire = 6

... with maternal granddam = 6

random effect no. = 1 NRM

no. of elements in NRM/GIN inverse 42

log determinant = -6.931471805599453

random effect no. = 2 IDE

no. of elements in NRM/GIN inverse 0

log determinant = 0.

======== end of file ============================13-03-2014==========01:13====

 

FixSolutions.out

 

======= Version 19-05-2012 ======================================= **KM** ======================================

 

Program WOMBAT : GLS solutions for fixed effects

================================================================================================================

 

Single Trait Model(with Maternal Effects) from Mrode, 2nd Edition, Example

 

 

Fixed effects for trait no. 1 "b_wt"

Effect Orig.code Level Solution S.Error SolSum=0 No.recs Eff.Mean

1 herd 1 1 3.23994 16.0492 -1.60674 4 30.000

1 herd 2 2 6.62640 17.8009 1.77971 3 33.000

1 herd 3 3 4.67372 18.0772 -0.172966 3 31.333

1 herd 4.84669

Effect Orig.code Level Solution S.Error SolSum=0 No.recs Eff.Mean

2 sex 1 1 0.00000 0.00000 3.42450 4 34.250 **

2 sex 2 2 -6.84900 15.2033 -3.42450 6 29.333

2 sex -3.42450

** marks effects which have been set to zero for the analysis

======== end of file ============================13-03-2014==========01:13======================================

 

 

RnSoln_animal+gmdam.dat 확인

 

Run N Original ID Tr Solution St.Error Ignore Inbr %

1 1 1 0.563890 12.0295 0.188 0.000

1 2 0.261565 9.30559 0.195

2 2 1 -1.24439 12.1701 0.112 0.000

2 2 -1.58316 9.18638 0.250

3 3 1 1.16494 11.7022 0.295 0.000

3 2 0.735732 9.16961 0.256

4 4 1 -0.484436 11.9673 0.213 0.000

4 2 0.585864 9.31881 0.187

5 5 1 0.629533 11.7098 0.293 0.000

5 2 -0.507471 9.15549 0.262

6 6 1 -0.858629 11.7172 0.291 0.000

6 2 0.841041 9.06603 0.295

7 7 1 -1.15597 11.8555 0.251 0.000

7 2 1.29932 9.22225 0.235

8 8 1 1.91740 11.6702 0.303 0.000

8 2 -0.157915 9.41532 0.123

9 9 1 -0.553263 11.7544 0.281 0.000

9 2 0.659541 9.39494 0.139

10 10 1 -1.05508 11.7728 0.276 0.000

10 2 -0.152954 9.38824 0.144

11 11 1 0.385358 12.4880 0.275 12.500

11 2 0.915958 9.90243 0.178

12 12 1 0.863317 12.3170 0.274 9.375

12 2 0.442008 9.87547 0.096

13 13 1 -2.97957 12.5438 0.260 12.500

13 2 0.930558E-01 10.0021 0.109

14 14 1 1.75130 12.8643 0.343 25.000

14 2 0.362213 10.3125 0.234

 

RnSoln_pedam.dat

 

Run N Original ID Tr Solution St.Error Ignore

1 2 1 -1.70083 5.88672 0.366

2 5 1 0.415397 6.17773 0.214

3 6 1 0.824915 5.90689 0.357

4 7 1 0.460519 6.08179 0.274

 

 

관련 파일

 

08_Maternal.zip