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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(print,ascn)
S3method(print,hscn)
S3method(print,hscnrna)
export("%>%")
export(BAFdistance)
export(HaplotypeHMM)
export(add_states)
export(alleleHMM)
export(assignHaplotypeHMM)
export(assign_bins_haplotypes)
export(assign_haplotype_label)
export(assign_label_persnp)
export(assign_states_dp)
export(assign_states_noprior)
export(assignalleleHMM)
export(callAlleleSpecificCN)
export(callAlleleSpecificCNfromHSCN)
export(callHaplotypeSpecificCN)
export(callalleleHMMcell)
export(combineBAFCN)
export(computehaplotypecounts)
export(consensuscopynumber)
export(coord_to_arm)
export(createBAFassay)
export(createCNmatrix)
export(createSNVmatrix)
export(create_cntransitions)
export(create_segments)
export(createbreakpointmatrix)
export(filter_segments)
export(filterbycells)
export(filtercn)
export(fix_assignments)
export(fixjitter)
export(format_haplotypes)
export(format_haplotypes_dlp)
export(format_haplotypes_rna)
export(format_tree_labels)
export(getBins)
export(get_clone_label_pos)
export(getphase)
export(hc_clustering)
export(is.ascn)
export(is.hscn)
export(is.hscnrna)
export(make_copynumber_legend)
export(map_to_segments)
export(missegregations)
export(missegregations_vscell)
export(orderdf)
export(per_arm_baf_mat)
export(per_chr_baf_plot)
export(per_chr_cn)
export(per_chrarm_cn)
export(per_segment_baf_mat)
export(per_segment_baf_plot)
export(phase_haplotypes)
export(phase_haplotypes_bychr)
export(phase_haplotypes_rna)
export(plotBAFperstate)
export(plotBBfit)
export(plotCNBAF)
export(plotCNprofile)
export(plotCNprofileBAF)
export(plotHeatmap)
export(plotHeatmapBAF)
export(plotSNVHeatmap)
export(plotSV)
export(plotSV2)
export(plotSVlines)
export(plot_clusters_used_for_phasing)
export(plot_proportions)
export(plot_umap)
export(plot_variance_state)
export(proportion_imbalance)
export(proportion_imbalance_manual)
export(qc_per_cell)
export(qc_summary)
export(rephasebins)
export(scBAFstate_cols)
export(scCN_cols)
export(scCNminorallele_cols)
export(scCNphase_cols)
export(scCNstate_cols)
export(segments_to_bins)
export(simulate_cell)
export(simulate_cells)
export(simulate_data_cohort)
export(singletons)
export(snv_states)
export(squashy_trans)
export(switchbins)
export(umap_clustering)
export(umap_clustering_breakpoints)
export(widen_bins)
export(widen_haplotypebins)
import(data.table)
importFrom(Rcpp,sourceCpp)
importFrom(data.table,":=")
importFrom(magrittr,"%>%")
useDynLib(signals)