PyPedal
An Open Source project
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1. Introduction
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1.2 Planned Features
1.1 Implemented Features
PyPedal is currently capable of the following operations:
Reading pedigree files in several formats;
Checking pedigree integrity (duplicate IDs, parents younger than offspring, etc.);
Generating summary information such as frequency of appearance in the pedigree file;
Computation of the numerator relationship matrix (
) from a pedigree file using the tabular method;
Inbreeding calculations for large pedigrees is provided courtesy of VanRaden's (1992) recursive algorithm;
Computation of average total and average individual coefficients of inbreeding and relationship;
Decomposition of
into
and
such that
;
Computation of the direct inverse of
(not accounting for inbreeding) using the method of Henderson (1976);
Computation of the direct inverse of
(accounting for inbreeding) using the method of Quaas (1976);
Storage of
and its inverse between user sessions as persistent Python objects using the pickle module to avoid unnecessary calculations;
Computation of effective founder number using the exact algorithm of Lacy (1989);
Computation of effective founder number using the approximate algorithm of Boichard et al. (1996);
Computation of effective ancestor number using the algorithm of Boichard et al. (1996);
Output to ASCII text files, including matrices, coefficients of inbreeding and relationship, and summary information;
Reordering and renumbering of pedigree files.
PyPedal
An Open Source project
Previous:
1. Introduction
Up:
1. Introduction
Next:
1.2 Planned Features
Release 2.0.0a1, documentation updated on April 08, 2004.