| Description |
1 online resource |
| Contents |
4.2.3 Recombination Maps in ibdsim2 -- Built-in maps -- Uniform maps -- 4.3 Variation in Realised Coefficients -- 4.3.1 First-Cousin Inbreeding -- 4.3.2 Some Siblings Are More Equal Than Others -- 4.4 Distributions of IBD Segments -- 4.4.1 The Importance of Sex -- 4.4.2 Separating the Inseparable: H-U-G -- 4.5 The Probability of No IBD Sharing -- Chapter 5: Probabilities on Pedigrees -- 5.1 Computing Pedigree Likelihoods -- 5.1.1 Basic Likelihood Calculations -- 5.1.2 The General Likelihood Expression -- 5.1.3 The Elston-Stewart Algorithm -- 5.1.4 Likelihoods With pedprobr -- 5.2 Factors Affecting Performance -- 5.2.1 Allele Lumping -- 5.2.2 Pedigree Loops -- 5.3 Likelihoods With Linked Markers -- 5.3.1 Linked Markers in R: Two Markers -- 5.3.2 Linked Markers in R: More Than Two Markers -- 5.4 Modelling Mutations -- 5.4.1 Properties of Mutation Models -- Reversibility -- Lumpability -- 5.5 Modelling Deviation From HWE -- 5.5.1 Founder Inbreeding -- 5.5.2 Theta Correction -- Chapter 6: Kinship Testing -- 6.1 Theory and Methods -- 6.1.1 Kinship Testing vs. Classical Hypothesis Testing -- 6.1.2 The Likelihood Ratio -- 6.1.3 Alternatives to LR -- 6.1.4 Kinship Testing With forrel -- 6.2 Paternity Testing -- 6.2.1 Manual Calculation of \LR -- 6.2.2 Paternity Testing With forrel -- 6.2.3 Direct Computation of \LR -- 6.3 A Relationship Riddle -- 6.4 Missing Person Identification -- 6.4.1 Terminology and Hypotheses -- 6.4.2 A Case Study -- 6.5 Power Analysis for Kinship Testing -- 6.5.1 Exclusion Power -- 6.5.2 Inclusion Power -- 6.5.3 Power Analysis for Missing Person Cases -- 6.6 Dealing With Mutations -- Chapter 7: Inference of Pairwise Relatedness -- 7.1 Maximum-Likelihood Estimation of Kappa -- 7.1.1 The Likelihood Function -- 7.1.2 The Maximum-Likelihood Estimate -- 7.1.3 Inadmissible Estimates? |
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7.1.4 What About the Kinship Coefficient? -- 7.2 Estimation of Identity Coefficients -- 7.3 ML Estimation in forrel -- 7.3.1 Example: The Relationship Riddle -- 7.3.2 Confidence and Uncertainty -- 7.4 Quality Control of Pedigree Data -- 7.5 Violating the Assumptions -- 7.5.1 Inaccurate Allele Frequencies -- 7.5.2 Linkage Between Markers -- 7.5.3 Inbreeding -- Chapter 8: Pedigree Reconstruction -- 8.1 Reconstruction by Pairwise Inference -- 8.2 Maximum-Likelihood Pedigree Reconstruction -- 8.2.1 Restrictions on the Space of Pedigrees -- 8.2.2 Solving the Relationship Riddle -- Chapter 9: Linkage Analysis -- 9.1 Theoretical Background -- 9.1.1 Hypothesis Testing and the LOD Score -- Example -- 9.1.2 Unknown Phase -- 9.1.3 Parametric Disease Models -- 9.1.4 What Is a Significant LOD Score? -- 9.1.5 Multipoint Analysis -- 9.1.6 Power Assessment -- 9.2 LOD Scores in paramlink2 -- 9.2.1 An X-Linked Example -- 9.2.2 More About the lod() Function -- Disease Models -- 9.3 A Case Study -- 9.3.1 Power Assessment -- 9.3.2 Loading the Data -- 9.3.3 Quality Control -- 9.3.4 Disease Model and Preliminary Analysis -- 9.3.5 Multipoint Analysis -- 9.3.6 Liability Classes -- 9.3.7 Summarising LOD Peaks -- Chapter 10: Segregation Analysis for Variant Interpretation -- 10.1 Background -- 10.2 The Bayes Factor -- 10.2.1 Using the Bayes Factor in the ACMG Framework -- 10.3 Bayes Factors With the segregatr Package -- 10.4 A Case Study -- Bibliography |
| Subject |
Forensic genetics -- Data processing
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Medical genetics -- Data processing
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R (Computer program language)
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R (Computer program language)
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| Form |
Electronic book
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| ISBN |
9780128245606 |
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0128245603 |
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