Breeding Insight Genomics Functions for Polyploid and Diploid
Species
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Documentation for package ‘BIGr’ version 0.7.2
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 |