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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(add_chunks)
export(add_error_rates)
export(annotate_and_filter)
export(avg_llr_cont)
export(avg_llr_loh)
export(bayesian_genotype)
export(bounded_freqs)
export(calculate_error_model)
export(calculate_ranked_predictions)
export(chr_stats)
export(combine_counts)
export(conta_ethnicity)
export(conta_graphics)
export(conta_llr)
export(conta_main)
export(conta_source)
export(conta_swap)
export(conta_threshold)
export(dbetabinom)
export(empty_result)
export(exclude_high_loh_regions)
export(factorize_chroms)
export(fail_test)
export(filter_data)
export(filter_gt_file)
export(fit_sens_by_conta_level)
export(genotype_concordance)
export(get_bases)
export(get_cumulative_sum)
export(get_ethnicity_priors)
export(get_exp_cf)
export(get_genomic_seq)
export(get_genomic_seqs)
export(get_genotype_concordance)
export(get_gt_likelihoods)
export(get_initial_loh_range)
export(get_initial_range)
export(get_lr)
export(get_per_bin_loh)
export(get_pregnancy_call)
export(get_s3_folders)
export(get_sample_name)
export(get_sex_call)
export(get_snp_intersection)
export(get_snp_likelihoods)
export(get_source_llr)
export(intersect_snps)
export(is_compatible_context)
export(l_loh)
export(ldbetabinom)
export(llr_cont)
export(llr_cont_all)
export(llr_loh)
export(llr_loh_all)
export(load_conta_file)
export(log_lr)
export(make_roc_plot_by_conta_level)
export(nloh)
export(optimize_after_grid)
export(optimize_likelihood)
export(parse_1000g_vcf)
export(parse_field)
export(pg)
export(pg2)
export(plot_avg_llr_by_conta)
export(plot_depth_by_chr)
export(plot_lr)
export(plot_lr_per_bin)
export(plot_max_likelihood)
export(plot_minor_ratio)
export(plot_ranked_predictions_per_chromosome)
export(plot_vfn_cp)
export(prep_1000g_vcf_af)
export(ratio_and_counts)
export(read_and_prep)
export(read_data_table)
export(read_gt_file)
export(read_sim_results)
export(read_vcf_dt)
export(sens_spec_by_level)
export(set_numeric_chrs)
export(sim_conta)
export(sim_data_to_roc)
export(simulate_loh_conta)
export(specify_precision)
export(ssig)
export(thresholds_by_sens_spec)
export(update_context)
export(write_data_table)
export(write_gt_file)
import(data.table)
import(ggplot2)
import(parallel)
importFrom(Rcpp,sourceCpp)
importFrom(data.table,fread)
importFrom(dplyr,"%>%")
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,count)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,inner_join)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,row_number)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,top_n)
importFrom(dplyr,transmute)
importFrom(grDevices,dev.off)
importFrom(grDevices,png)
importFrom(graphics,abline)
importFrom(graphics,plot)
importFrom(pROC,ggroc)
importFrom(pROC,roc)
importFrom(readr,read_tsv)
importFrom(readr,write_tsv)
importFrom(reshape2,melt)
importFrom(stats,dbinom)
importFrom(stats,optimize)
importFrom(stats,quantile)
importFrom(stats,rpois)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,weighted.mean)
importFrom(tidyr,drop_na)
importFrom(tidyr,gather)
importFrom(tidyr,spread)
importFrom(utils,capture.output)
importFrom(utils,packageVersion)
importFrom(utils,write.table)
useDynLib(conta)