Package index • numbat

Preparing data

aggregate_counts(): Utility function to make reference gene expression profiles

CNV detection

get_bulk(): Aggregate single-cell data into combined bulk expression and allele profile

analyze_bulk(): Call CNVs in a pseudobulk profile using the Numbat joint HMM

detect_clonal_loh(): Call clonal LOH using SNP density. Rcommended for cell lines or tumor samples with no normal cells.

Single-cell clonal decomposition

run_numbat(): Run workflow to decompose tumor subclones

Visualizing results

Numbat: Numbat R6 class

get_gtree(): Get a tidygraph tree with simplified mutational history.

plot_bulks(): Plot a group of pseudobulk HMM profiles

plot_consensus(): Plot consensus CNVs

plot_exp_roll(): Plot single-cell smoothed expression magnitude heatmap

plot_mut_history(): Plot mutational history

plot_phylo_heatmap(): Plot single-cell CNV calls along with the clonal phylogeny

plot_psbulk(): Plot a pseudobulk HMM profile

plot_sc_tree(): Plot single-cell smoothed expression magnitude heatmap

cnv_heatmap(): Plot CNV heatmap

Example data

df_allele_example: example allele count dataframe

count_mat_example: example gene expression count matrix

ref_hca: reference expression magnitudes from HCA

ref_hca_counts: reference expression counts from HCA

bulk_example: example pseudobulk dataframe

annot_ref: example reference cell annotation

count_mat_ref: example reference count matrix

gexp_roll_example: example smoothed gene expression dataframe

hc_example: example hclust tree

joint_post_example: example joint single-cell cnv posterior dataframe

mut_graph_example: example mutation graph

phylogeny_example: example single-cell phylogeny

pre_likelihood_hmm: HMM object for unit tests

segs_example: example CNV segments dataframe

Genome annotations

acen_hg19: centromere regions (hg19)

acen_hg38: centromere regions (hg38)

chrom_sizes_hg19: chromosome sizes (hg19)

chrom_sizes_hg38: chromosome sizes (hg38)

gaps_hg19: genome gap regions (hg19)

gaps_hg38: genome gap regions (hg38)

gtf_hg19: gene model (hg19)

gtf_hg38: gene model (hg38)

gtf_mm10: gene model (mm10)

vcf_meta: example VCF header

Misc

annotate_genes(): Annotate genes on allele dataframe

upgma(): UPGMA and WPGMA clustering