Package index • signals

All functions
`CNbins`	Copy number bins for DLP+ cells
`CNmetrics`	Per-cell quality control metrics
`SNV`	SNV counts for DLP+ cells
`SVs`	Structural variants for cell line SA921
`add_gene_locations_to_seurat()`	Add gene genomic location to seurat object
`callAlleleSpecificCN()`	Call allele specific copy number in single cell datasets
`callAlleleSpecificCNfromHSCN()`	Call allele specific copy number in single cell datasets
`callHaplotypeSpecificCN()`	Call haplotype specific copy number in single cell datasets
`combineBAFCN()`	Combine copy number bins with haplotype data
`computehaplotypecounts()`	Compute phasing using top imbalanced cells
`coord_to_arm()`	Genomic coordinate to chromosome arm
`countsmatrix`	Gene expression counts matrix
`createCNmatrix()`	Create copy number matrix for heatmap visualization
`format_haplotypes()`	Format and phase haplotypes
`format_haplotypes_dlp()`	Format haplotypes from DLP+ data
`getBins()`	Make fixed-width bins
`get_centromere_bins()`	Get centromeric bins
`get_sv_lines_and_arcs_legend()`	Get SV Orientation Legend for lines_and_arcs Style
`haplotypes`	Haplotype block allele counts for DLP+ cells
`haplotypes_rna`	Haplotype allele counts for scRNA cells
`hc_clustering()`	Hierarchical clustering (deprecated)
`leiden_clustering()`	Perform PCA + kNN graph + Leiden clustering on copy number data
`phase_haplotypes()`	Phase haplotypes using distribution method
`plotBAFperstate()`	Plot BAF distributions per allele specific state
`plotCNprofile()`	Plot a single cell copy number profile
`plotCNprofileBAF()`	Plot a single cell allele specific copy number profile
`plotHeatmap()`	Heatmap plot
`plot_clusters_used_for_phasing()`	Plot clusters used for phasing
`rephasebins()`	Rephase haplotype copy number
`scale_color_scCN()`	Colour scale constructor for scCN (single cell Copy Number) colors
`scale_fill_scCN()`	Fill scale constructor for scCN (single cell Copy Number) colors
`umap_clustering()`	Perform UMAP dimensionality reduction and HDBSCAN clustering on copy number data

Reference

All functions