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Genome-Wide Association Studies and Genomic Prediction

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Cover of 'Genome-Wide Association Studies and Genomic Prediction'

Table of Contents

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    Book Overview
  2. Altmetric Badge
    Chapter 1 R for genome-wide association studies.
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    Chapter 2 Descriptive statistics of data: understanding the data set and phenotypes of interest.
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    Chapter 3 Designing a GWAS: Power, Sample Size, and Data Structure.
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    Chapter 4 Managing Large SNP Datasets with SNPpy.
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    Chapter 5 Quality control for genome-wide association studies.
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    Chapter 6 Overview of Statistical Methods for Genome-Wide Association Studies (GWAS).
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    Chapter 7 Statistical analysis of genomic data.
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    Chapter 8 Using PLINK for Genome-Wide Association Studies (GWAS) and Data Analysis.
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    Chapter 9 Genome-Wide Complex Trait Analysis (GCTA): Methods, Data Analyses, and Interpretations
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    Chapter 10 Bayesian Methods Applied to GWAS.
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    Chapter 11 Implementing a QTL Detection Study (GWAS) Using Genomic Prediction Methodology.
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    Chapter 12 Genome-Enabled Prediction Using the BLR (Bayesian Linear Regression) R-Package.
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    Chapter 13 Genomic Best Linear Unbiased Prediction (gBLUP) for the Estimation of Genomic Breeding Values.
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    Chapter 14 Detecting regions of homozygosity to map the cause of recessively inherited disease.
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    Chapter 15 Use of ancestral haplotypes in genome-wide association studies.
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    Chapter 16 Genotype phasing in populations of closely related individuals.
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    Chapter 17 Genotype Imputation to Increase Sample Size in Pedigreed Populations
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    Chapter 18 Validation of Genome-Wide Association Studies (GWAS) Results.
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    Chapter 19 Detection of Signatures of Selection Using F ST.
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    Chapter 20 Association weight matrix: a network-based approach towards functional genome-wide association studies.
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    Chapter 21 Mixed effects structural equation models and phenotypic causal networks.
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    Chapter 22 Epistasis, complexity, and multifactor dimensionality reduction.
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    Chapter 23 Applications of Multifactor Dimensionality Reduction to Genome-Wide Data Using the R Package 'MDR'.
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    Chapter 24 Higher order interactions: detection of epistasis using machine learning and evolutionary computation.
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    Chapter 25 Incorporating prior knowledge to increase the power of genome-wide association studies.
  27. Altmetric Badge
    Chapter 26 Genome-Wide Association Studies and Genomic Prediction
Attention for Chapter 8: Using PLINK for Genome-Wide Association Studies (GWAS) and Data Analysis.
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Chapter title
Using PLINK for Genome-Wide Association Studies (GWAS) and Data Analysis.
Chapter number 8
Book title
Genome-Wide Association Studies and Genomic Prediction
Published in
Methods in molecular biology, May 2013
DOI 10.1007/978-1-62703-447-0_8
Pubmed ID
Book ISBNs
978-1-62703-446-3, 978-1-62703-447-0
Authors

Miguel E. Rentería, Adrian Cortes, Sarah E. Medland

Editors

Cedric Gondro, Julius van der Werf, Ben Hayes

Abstract

Within this chapter we introduce the basic PLINK functions for reading in data, applying quality control, and running association analyses. Three worked examples are provided to illustrate: data management and assessment of population substructure, association analysis of a quantitative trait, and qualitative or case-control association analyses.

X Demographics

X Demographics

The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 107 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 2 2%
Colombia 1 <1%
Australia 1 <1%
Switzerland 1 <1%
United Kingdom 1 <1%
Brazil 1 <1%
Unknown 100 93%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 28 26%
Researcher 18 17%
Student > Master 15 14%
Student > Bachelor 9 8%
Student > Doctoral Student 7 7%
Other 10 9%
Unknown 20 19%
Readers by discipline Count As %
Agricultural and Biological Sciences 45 42%
Biochemistry, Genetics and Molecular Biology 19 18%
Computer Science 8 7%
Medicine and Dentistry 6 6%
Social Sciences 3 3%
Other 6 6%
Unknown 20 19%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 13 June 2013.
All research outputs
#18,340,012
of 22,711,645 outputs
Outputs from Methods in molecular biology
#7,851
of 13,079 outputs
Outputs of similar age
#145,535
of 193,691 outputs
Outputs of similar age from Methods in molecular biology
#20
of 32 outputs
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