BIGr/NAMESPACE at main · Breeding-Insight/BIGr · GitHub

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# Generated by roxygen2: do not edit by hand

export(allele_freq_poly)
export(calculate_Het)
export(calculate_MAF)
export(check_homozygous_trios)
export(check_madc_sanity)
export(check_ped)
export(check_replicates)
export(dosage2vcf)
export(dosage_ratios)
export(filterMADC)
export(filterVCF)
export(find_parentage)
export(flip_dosage)
export(get_countsMADC)
export(imputation_concordance)
export(madc2gmat)
export(madc2vcf_all)
export(madc2vcf_multi)
export(madc2vcf_targets)
export(merge_MADCs)
export(solve_composition_poly)
export(thinSNP)
export(updog2vcf)
export(validate_pedigree)
import(dplyr)
import(janitor)
import(parallel)
import(quadprog)
import(stringr)
import(tibble)
import(tidyr)
import(vcfR)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,reverseComplement)
importFrom(Rdpack,reprompt)
importFrom(Rsamtools,bgzip)
importFrom(data.table,CJ)
importFrom(data.table,as.data.table)
importFrom(data.table,copy)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(data.table,rbindlist)
importFrom(data.table,set)
importFrom(dplyr,"%>%")
importFrom(dplyr,across)
importFrom(dplyr,arrange)
importFrom(dplyr,case_when)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,group_modify)
importFrom(dplyr,mutate)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,ungroup)
importFrom(dplyr,where)
importFrom(pwalign,nucleotideSubstitutionMatrix)
importFrom(pwalign,pairwiseAlignment)
importFrom(readr,read_csv)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(rlang,sym)
importFrom(stats,cor)
importFrom(stats,reorder)
importFrom(stats,setNames)
importFrom(tibble,as_tibble)
importFrom(utils,packageVersion)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(utils,tail)
importFrom(utils,write.csv)
importFrom(utils,write.table)
importFrom(vcfR,extract.gt)
importFrom(vcfR,maf)
importFrom(vcfR,read.vcfR)
importFrom(vcfR,write.vcf)