BIGpopA 2.0.0
find_parentage() and validate_pedigree()
now support any ploidy through a new ploidy argument
(default 2). Genotypes may be coded as allele-B dosage (0, 1, …,
ploidy).- Even ploidy uses a generalized polysomic gamete-range Mendelian
test; it is exact for autopolyploids and conservative for allopolyploids
(correct trios are never wrongly flagged).
- Odd ploidy (e.g. triploid), where balanced gametes are undefined,
automatically falls back to a model-free opposite-homozygote exclusion
evaluated on homozygous-informative markers only.
- Diploid results (
ploidy = 2) are unchanged from
previous versions.
BIGpopA 1.0.6
- Added a “BIGpopA Tutorial” vignette demonstrating the pedigree
cleaning, validation, parentage assignment, and breed/line composition
workflow
BIGpopA 1.0.5
- Updated package title and example on function descriptions to pass
CRAN review
BIGpopA 1.0.4
- Removed LICENSE file to pass CRAN automated tests
BIGpopA 1.0.3
- Fixed typo on repo name and patched find_parentage
- Removed /dev from repository
- Added words to WORDLIST
BIGpopA 1.0.2
- Renamed package to BIGpopA and made repo public
popR 1.0.2
- Initial release of
BIGpopA as a standalone
package.
BIGpopA contains pedigree validation and breed/line
composition functions previously found in BIGr, where they
will no longer be maintained going forward.- These functions are the backbone of the pedigree and composition
modules in the familia Shiny
app.
Functions included
check_ped() — checks and corrects common pedigree
errors (duplicate rows, conflicting trios, missing parents, cycles,
inconsistent sex roles)find_parentage() — assigns most likely parent(s) to
progeny using Mendelian error rates or homozygous mismatch ratesvalidate_pedigree() — validates parent-offspring trios
against SNP genotype data and outputs a corrected pedigreeallele_freq_poly() — computes allele frequencies for
diploid and polyploid reference populationssolve_composition_poly() — estimates genome-wide
breed/line composition using quadratic programming