# Breeding Insight Genomics Functions for Polyploid and Diploid Species

## Documentation for package ‘BIGr’ version 0.7.2

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

allele_freq_poly | Compute Allele Frequencies for Populations
calculate_Het | Calculate Observed Heterozygosity from a Genotype Matrix
calculate_MAF | Calculate Minor Allele Frequency from a Genotype Matrix
check_homozygous_trios | Check Homozygous Loci in Trios
check_madc_sanity | Run basic sanity checks on a MADC-style allele report
check_ped | Check a pedigree file for accuracy and report/correct common errors
check_replicates | Compatibility Between Samples Genotypes
dosage2vcf | Convert DArTag genotype reports and counts to VCF
dosage_ratios | Calculate the Percentage of Each Dosage Value
filterMADC | Filter MADC Files
filterVCF | Filter a VCF file
find_parentage | Find Parentage Assignments for Progeny
flip_dosage | Switch Dosage Values from a Genotype Matrix
get_countsMADC | Obtain Read Counts from MADC File
imputation_concordance | Calculate Concordance between Imputed and Reference Genotypes
madc2gmat | Convert MADC Files to an Additive Genomic Relationship Matrix
madc2vcf_all | Converts MADC file to VCF recovering target and off-target SNPs
madc2vcf_multi | Convert MADC file to VCF using polyRAD for multiallelic genotyping
madc2vcf_targets | Format MADC Target Loci Read Counts Into VCF
merge_MADCs | Merge MADC files
solve_composition_poly | Compute Genome-Wide Breed Composition
thinSNP | Thin a dataframe of SNPs based on genomic position
updog2vcf | Export Updog Results as VCF
validate_pedigree | Validate Pedigree Trios Using Mendelian Error Analysis