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.

Release on GitHub · About BIGpopA