Breeding Insight Genomics Functions for Polyploid and Diploid
Species
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Documentation for package ‘BIGr’ version 0.5.5
Help Pages
| 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_ped | Evaluate Pedigree File for Accuracy |
| check_replicates | Compatibility Between Samples Genotypes |
| dosage2vcf | Convert DArTag Dosage and Counts to VCF |
| dosage_ratios | Calculate the Percentage of Each Dosage Value |
| filterVCF | Filter a VCF file |
| 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 |
| madc2vcf_all | Converts MADC file to VCF recovering target and off-target SNPs |
| madc2vcf_targets | Format MADC Target Loci Read Counts Into VCF |
| merge_MADCs | Merge MADC files |
| updog2vcf | Export Updog Results as VCF |