pydigree

A python3 package for operations on pedigree and genotype data, including simulation of genotype-phenotype associations under quantitative genetic models

Requires: Python 3.4+, numpy, scipy, pandas, cython

Submodules

In addition to basic pedigree data manipulation, pydigree also includes submodules for more complicated tasks:

• simulation: Provides classes for simulating genetic data
• stats: Classes and functions for statistical genetics
• mixedmodel: Provides classes for using mixed models with family data
• io: Provides functions for importing/exporting data from common data formats, including:
• plink: Functions for working with plink format PED/MAP data
• vcf: Functions for working with the VCF genotype format
• genomesimla: Includes a function for reading genomeSIMLA format chromosome templates
• sgs: Functions for shared genomic segment data

Classes

• Invidiual: Models an individual with pedigree and phenotype data
• Population: Models groups of Individuals with a common genetic background
• Pedigree: A special case of Population for related individuals. Implements kinship/inbreeding functions
• PedigreeCollection: A container class handling multiple pedigrees
• ChromosomeTemplate: Models a chromosome with information on allele frequency and marker position
• ChromosomeSet: The set of ChromosomeTemplates for a population
• Alleles: Stores a haploid set of alleles
• SparseAlleles: Stores a haploid set of alleles as differences from a reference
• LabelledAlleles: An efficient container for storing references to a founder chromosome
• MixedModel: A class for fitting mixed-effect models with related individuals
• MLEResult: A class containing the maximum likelihood estimates of parameters and values pertaining to the likelihood function at the MLE
• Architecture: A class describing the genetic architecture for a trait to be used in simulation
• GeneDroppingSimulation: A base class from which other gene-drop simulation objects inherit
• NaiveGeneDroppingSimulation: Simulates genetic data for pedigrees by random gene dropping
• ConstrainedMendelianSimulation: Simulates genetic data for pedigrees from a prespecified inheritance structure
• SGSAnalysis: A class containing the result of a shared genomic segment (SGS) analysis
• SGS: A class containing the segments shared between a pair of individuals
• Segment: A class describing the location of a shared segment between a pair of individuals

Exceptions

• IterationError: Raised when at iterative algorithm exceeds the maximum allowed number of iterations
• NotMeaningfulError: Raised when a comparison does not make sense (e.g. is one genotype greater than the other)
• SimulationError: Raised when an error occurs in a simulation
• FileFormatError: Raised when an input file can't be parsed successfully

Scripts

Pydigree includes a few useful scripts for dealing with pedigree data including:

• simulate_pedigree_data.py: Simulates data from template pedigrees
• bitsize.py: Calculates bit sizes for each pedigree
• kinship.py: Caluclates inbreeding coefficients and pairwise kinship coefficients for pedigrees
• genedrop.py: Performs gene dropping simulations to approximate the actual probability of an IBD configuration
• polygenic.py: Calculates variance components for normally distributed continuous traits.

Citation

J.E. Hicks (2017) Pydigree: a python module for manipulation and simulation and of genetic datasets. biorxiv preprint doi:10.1101/213413

References

Pedigrees

• Charles II of Spain: http://en.wikipedia.org/wiki/Charles_II_of_Spain