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Table 3 Summary of LOD scores for the three penetrance models

From: MLEP: an R package for exploring the maximum likelihood estimates of penetrance parameters

Disease allele frequency

Model

Recombination fraction(θ)

True value

Assumed value

0

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

0.0001

 

True

4.071

3.831

3.535

3.201

2.835

2.438

2.011

1.553

1.066

0.549

0.0001

MLE

3.992

3.797

3.520

3.198

2.838

2.444

2.017

1.559

1.069

0.550

 

Dominant

-0.158

3.296

3.394

3.240

2.965

2.609

2.189

1.714

1.189

0.617

 

True

4.065

3.826

3.530

3.196

2.830

2.434

2.007

1.550

1.063

0.547

0.001

MLE

4.003

3.805

3.527

3.204

2.843

2.448

2.021

1.561

1.071

0.550

 

Dominant

-0.188

3.265

3.364

3.211

2.939

2.586

2.170

1.698

1.176

0.609

 

True

4.022

3.784

3.489

3.157

2.792

2.398

1.974

1.521

1.040

0.532

0.01

MLE

3.984

3.780

3.500

3.175

2.815

2.421

1.995

1.538

1.051

0.538

 

Dominant

-0.234

3.217

3.320

3.171

2.902

2.552

2.138

1.670

1.155

0.598

 

True

3.702

3.474

3.191

2.872

2.524

2.150

1.750

1.328

0.887

0.437

0.1

MLE

3.665

3.429

3.143

2.823

2.476

2.103

1.708

1.292

0.860

0.422

 

Dominant

-0.425

3.040

3.146

3.002

2.738

2.397

1.997

1.549

1.059

0.534

 

True

3.257

3.049

2.787

2.492

2.171

1.827

1.464

1.087

0.704

0.331

0.25

MLE

1.524

1.407

1.270

1.121

0.964

0.800

0.634

0.467

0.303

0.146

 

Dominant

-0.743

2.748

2.862

2.727

2.478

2.158

1.783

1.362

0.906

0.437

 

True

2.549

2.384

2.165

1.917

1.646

1.359

1.061

0.760

0.469

0.205

0.5

MLE

-0.009

0.204

0.292

0.321

0.315

0.284

0.238

0.182

0.121

0.059

 

Dominant

-1.339

2.208

2.349

2.250

2.044

1.765

1.434

1.067

0.682

0.311

0.001

 

True

4.086

3.846

3.548

3.213

2.846

2.447

2.019

1.560

1.070

0.551

0.0001

MLE

4.008

3.812

3.534

3.210

2.849

2.453

2.025

1.565

1.073

0.552

 

Dominant

-0.140

3.312

3.409

3.253

2.977

2.619

2.198

1.721

1.193

0.619

 

True

4.081

3.841

3.543

3.208

2.841

2.443

2.014

1.556

1.067

0.549

0.001

MLE

4.018

3.820

3.541

3.216

2.854

2.458

2.028

1.567

1.075

0.553

 

Dominant

-0.170

3.281

3.379

3.225

2.951

2.597

2.179

1.705

1.180

0.611

 

True

4.038

3.799

3.502

3.169

2.803

2.407

1.981

1.527

1.044

0.534

0.01

MLE

4.000

3.795

3.513

3.187

2.825

2.429

2.002

1.543

1.055

0.540

 

Dominant

-0.216

3.234

3.335

3.185

2.915

2.563

2.147

1.677

1.160

0.601

 

True

3.717

3.489

3.204

2.884

2.535

2.159

1.757

1.334

0.891

0.439

0.1

MLE

3.602

3.338

3.040

2.717

2.372

2.006

1.621

1.221

0.809

0.394

 

Dominant

-0.407

3.056

3.161

3.016

2.751

2.407

2.006

1.556

1.064

0.536

 

True

3.272

3.063

2.800

2.503

2.181

1.836

1.471

1.093

0.708

0.332

0.25

MLE

1.847

1.667

1.479

1.286

1.090

0.893

0.698

0.508

0.325

0.154

 

Dominant

-0.725

2.765

2.877

2.741

2.490

2.168

1.792

1.369

0.911

0.439

 

True

2.563

2.397

2.177

1.927

1.655

1.366

1.067

0.765

0.471

0.207

0.5

MLE

0.048

0.234

0.310

0.332

0.321

0.288

0.240

0.183

0.121

0.060

 

Dominant

-1.321

2.225

2.364

2.264

2.056

1.776

1.443

1.073

0.686

0.312

0.01

 

True

3.808

3.619

3.348

3.038

2.694

2.317

1.909

1.472

1.008

0.517

0.0001

MLE

3.647

3.461

3.206

2.913

2.588

2.231

1.841

1.421

0.973

0.499

 

Dominant

-0.374

3.002

3.150

3.037

2.794

2.466

2.072

1.621

1.122

0.580

 

True

3.863

3.639

3.355

3.038

2.691

2.313

1.905

1.469

1.005

0.515

0.001

MLE

3.730

3.532

3.267

2.964

2.628

2.262

1.864

1.437

0.983

0.503

 

Dominant

-0.345

3.011

3.136

3.013

2.770

2.444

2.053

1.605

1.109

0.572

 

True

3.881

3.637

3.344

3.018

2.664

2.284

1.876

1.442

0.983

0.501

0.01

MLE

3.836

3.623

3.344

3.026

2.677

2.299

1.891

1.455

0.992

0.505

 

Dominant

-0.329

3.019

3.133

2.998

2.746

2.417

2.025

1.579

1.089

0.562

 

True

3.629

3.389

3.101

2.782

2.436

2.067

1.677

1.268

0.844

0.415

0.1

MLE

3.514

3.243

2.944

2.622

2.281

1.922

1.548

1.162

0.767

0.374

 

Dominant

-0.455

2.907

3.021

2.884

2.628

2.297

1.909

1.478

1.008

0.508

 

True

3.224

3.002

2.734

2.437

2.115

1.775

1.418

1.050

0.679

0.319

0.25

MLE

2.100

1.888

1.668

1.445

1.219

0.993

0.772

0.557

0.354

0.166

 

Dominant

-0.737

2.651

2.774

2.647

2.405

2.093

1.728

1.320

0.879

0.426

 

True

2.563

2.384

2.158

1.905

1.632

1.345

1.049

0.752

0.465

0.205

0.5

MLE

-0.105

0.150

0.249

0.286

0.286

0.262

0.221

0.170

0.114

0.056

 

Dominant

-1.289

2.160

2.311

2.219

2.018

1.746

1.422

1.062

0.684

0.315

0.1

 

True

2.571

3.140

2.984

2.742

2.445

2.105

1.730

1.326

0.900

0.457

0.0001

MLE

2.645

2.809

2.691

2.494

2.245

1.955

1.632

1.276

0.886

0.460

 

Dominant

-3.354

2.123

2.564

2.607

2.467

2.211

1.869

1.462

1.005

0.513

 

True

2.965

3.191

3.011

2.753

2.447

2.103

1.727

1.323

0.897

0.455

0.001

MLE

2.986

3.054

2.898

2.663

2.377

2.051

1.692

1.304

0.891

0.456

 

Dominant

-2.980

2.115

2.538

2.580

2.442

2.189

1.850

1.446

0.991

0.504

 

True

3.319

3.265

3.044

2.763

2.441

2.086

1.705

1.300

0.877

0.442

0.01

MLE

3.223

3.185

2.991

2.731

2.423

2.077

1.701

1.299

0.876

0.441

 

Dominant

-2.599

2.149

2.524

2.555

2.415

2.161

1.823

1.420

0.971

0.495

 

True

3.388

3.185

2.916

2.609

2.274

1.915

1.538

1.149

0.754

0.366

0.1

MLE

3.350

3.133

2.859

2.551

2.218

1.863

1.492

1.111

0.727

0.351

 

Dominant

-2.344

2.159

2.479

2.473

2.314

2.051

1.713

1.320

0.894

0.446

 

True

3.111

2.897

2.627

2.327

2.003

1.662

1.311

0.956

0.608

0.283

0.25

MLE

2.471

2.224

1.967

1.702

1.434

1.165

0.900

0.644

0.403

0.186

 

Dominant

-2.443

1.991

2.296

2.283

2.120

1.861

1.536

1.169

0.774

0.372

 

True

2.561

2.370

2.128

1.859

1.573

1.276

0.978

0.688

0.419

0.184

0.5

MLE

0.240

0.324

0.351

0.344

0.315

0.271

0.217

0.160

0.102

0.048

 

Dominant

-2.804

1.584

1.892

1.894

1.751

1.522

1.244

0.929

0.596

0.275

0.2

 

True

1.245

2.462

2.452

2.312

2.096

1.827

1.517

1.174

0.804

0.412

0.0001

MLE

1.471

2.049

2.086

2.006

1.852

1.641

1.383

1.086

0.754

0.392

 

Dominant

-5.718

1.358

1.978

2.131

2.078

1.898

1.628

1.290

0.898

0.465

 

True

1.891

2.542

2.488

2.325

2.099

1.826

1.514

1.171

0.801

0.410

0.001

MLE

2.027

2.354

2.310

2.174

1.976

1.730

1.444

1.122

0.772

0.397

 

Dominant

-5.102

1.341

1.948

2.100

2.048

1.869

1.602

1.268

0.883

0.458

 

True

2.484

2.669

2.544

2.343

2.094

1.808

1.491

1.147

0.781

0.397

0.01

MLE

2.435

2.557

2.448

2.263

2.030

1.757

1.451

1.116

0.759

0.385

 

Dominant

-4.507

1.360

1.924

2.059

1.997

1.816

1.552

1.227

0.851

0.436

 

True

2.763

2.662

2.461

2.218

1.944

1.647

1.332

1.002

0.663

0.323

0.1

MLE

2.684

2.539

2.326

2.081

1.813

1.526

1.226

0.916

0.602

0.291

 

Dominant

-4.074

1.352

1.847

1.951

1.876

1.694

1.435

1.117

0.756

0.379

 

True

2.570

2.425

2.215

1.972

1.705

1.423

1.128

0.828

0.529

0.246

0.25

MLE

1.948

1.755

1.551

1.341

1.128

0.916

0.707

0.506

0.317

0.146

 

Dominant

-4.071

1.211

1.691

1.789

1.717

1.540

1.290

0.986

0.657

0.320

 

True

2.101

1.964

1.775

1.560

1.328

1.085

0.837

0.591

0.360

0.159

0.5

MLE

0.625

0.595

0.545

0.484

0.416

0.343

0.269

0.195

0.125

0.060

 

Dominant

-4.299

0.868

1.353

1.466

1.413

1.260

1.039

0.781

0.509

0.239

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BMC Research Notes

ISSN: 1756-0500

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