Population genetics and genomics in R
  • Table of contents
  • Part I
    • Introduction
    • Getting ready to use R
  • Part II
    • Data preparation
    • First steps
    • Population strata and clone correction
    • Locus-based statistics and missing data
    • Genotypic evenness, richness, and diversity
    • Linkage disequilibrium
    • Population structure
    • Minimum Spanning Networks
    • AMOVA
    • Discriminant analysis of principal components (DAPC)
  • Part III
    • Population genomics and HTS
    • Reading VCF data
    • Analysis of genomic data
    • Analysis of GBS data
    • Clustering plot
  • Workshops
    • ICPP
      • Preparation
      • Introduction
      • VCF data
      • Quality control
      • Analysis of GBS data
      • Analysis of genome data
    • APS Southern Division
      • Preparation
      • Introduction
      • VCF data
      • Quality control
      • Analysis of GBS data
  • About
    • Authors
  • Appendices
    • Introduction to R
    • Data sets
    • Function glossary
    • Background_functions
    • Source Code

Table of contents

  • Part I:
    • Introduction
    • Getting ready to use R
  • Part II: Using traditional markers for population genetic analysis
    • First analysis
    • Population strata and clone correction
    • Locus-based statistics and missing data
    • Genotypic evenness, richness, and diversity
    • Linkage disequilibrium
    • Population structure
    • Minimum Spanning Networks
    • AMOVA
    • Discriminant analysis of principal components (DAPC)
  • Part III: Using genomic data in population genetics
    • Population genomics based on high throughut sequencing (HTS)
    • Reading VCF data
    • Quality control
    • Analysis of genomic data
    • Analysis of GBS data
  • About
    • About the authors
  • Appendices
    • Data sets
    • Function glossary
    • Source code for this primer
    • Introduction to R