Nuts and bolts

In this tutorial we’ll learn about the basic data structures used for representing genotype and phenotype data.

• Indexing
  • Component indexing
    • Overview
    • Constructing a component index from a cartestian product
    • Constructing a component index for specific components
    • Constructing a generic component index
  • Variant indexing
    • Constructing a variant index
    • Switching between haploid and diploid indices
  • Sample indexing
    • Constructing a generic sample index
    • Constructing a sample index for specific iids and fids
    • Constructing a sample index with a DataFrame
• Data structures
  • Phenotype arrays
    • Retrieving index objects
    • Subsetting phenotype arrays
    • Conversion to Pandas
  • Haplotype arrays
    • Retrieving index objects
    • Computing empirical allele frequencies
    • Interpolating genetic distances