The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

BIGpopA 2.1.0

• New vcf_to_dosage() converts a VCF (.vcf / .vcf.gz) or vcfR object into allele-B dosages for any ploidy, as an id + markers table or an individuals x markers matrix.
• New ped_to_dosage() converts a PLINK .ped file (diploid) into allele dosages. A .map file is optional and only supplies marker names. The counted allele is the alphabetically/numerically last allele at each marker, or can be supplied to code a second file like a first one.
• find_parentage(), validate_pedigree(), allele_freq_poly() and solve_composition_poly() now accept genotypes as a TXT/TSV/CSV file, a VCF file or vcfR object, a PLINK .ped file, a data.frame / data.table, or a matrix. VCF input is converted with vcf_to_dosage() using the function’s ploidy; .ped input requires ploidy = 2.
• When the reference panel is a .ped file, allele_freq_poly() stores the counted allele per marker and solve_composition_poly() uses it to code a validation .ped file consistently.
• allele_freq_poly() and solve_composition_poly() also accept a data.frame with an id / ID column; existing matrix and row-named data.frame inputs are unchanged.
• Genotype read errors in find_parentage() and validate_pedigree() now include the underlying error message.
• Column names id, male_parent, female_parent and sex are now matched ignoring case, spaces and dots (e.g. ID, Male_Parent, FEMALE PARENT) in check_ped(), validate_pedigree(), find_parentage() and genotype tables.
• Fixed solve_composition_poly() failing when Y contains a single animal.
• Removed the ped, groups, mia, sire and dam arguments from solve_composition_poly(). They relied on internal helpers that were not carried over from BIGr and always failed. The function now takes Y, X and ploidy.

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 rates
• validate_pedigree() — validates parent-offspring trios against SNP genotype data and outputs a corrected pedigree
• allele_freq_poly() — computes allele frequencies for diploid and polyploid reference populations
• solve_composition_poly() — estimates genome-wide breed/line composition using quadratic programming

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.