NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(format,RefphaseOutput)
S3method(plot,RefphaseOutput)
S3method(print,RefphaseOutput)
export(center_baf)
export(check_for_errors_in_analysis_groups)
export(delete_checkpoint)
export(export)
export(fit_logr_to_ascat)
export(get_checkpoint)
export(horizontal_phasing)
export(horizontal_phasing_for_output)
export(horizontal_phasing_just_segments)
export(horizontal_phasing_just_segments_per_sample)
export(horizontal_phasing_segment_file)
export(intersect_all_snps)
export(make_group_phased_segs_grange_list)
export(make_group_phased_segs_w_cn_calls_list)
export(make_group_summaries_list)
export(plot_all_chromosomes)
export(plot_analysis_across_groups_summary_cn_tracks)
export(plot_analysis_groups_allele_specific_cn_summary_tracks)
export(plot_analysis_two_way_group_comparison_summary)
export(plot_analysis_within_groups_summary_cn_tracks)
export(plot_chromosome)
export(plot_genome)
export(plot_group_summaries)
export(plot_patient_summary)
export(plot_single_track)
export(put_checkpoint)
export(refphase)
export(refphase_load)
export(refphase_load_legacy)
export(refphase_load_segments_tsv)
export(round_copy_numbers)
export(run_ascat_for_refphase)
export(sort_haplotypes)
export(sort_haplotypes_just_segs)
export(sort_haplotypes_just_segs_per_sample)
export(write_patient_summary)
export(write_segs)
export(write_snps)
import(GenomicRanges)
import(IRanges)
import(S4Vectors)
import(data.table)
import(dplyr)
import(graphics)
import(mclust)
import(methods)
import(readr)
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,mcols)
importFrom(IRanges,subsetByOverlaps)
importFrom(diptest,dip)
importFrom(diptest,dip.test)
importFrom(e1071,naiveBayes)
importFrom(logging,logdebug)
importFrom(logging,loginfo)
importFrom(logging,setLevel)
importFrom(magrittr,"%>%")
importFrom(mclust,Mclust)
importFrom(readr,write_tsv)
importFrom(stats,optim)
importFrom(utils,write.table)