Man pages for whtns/numbat
Haplotype-Aware CNV Analysis from scRNA-Seq
| acen_hg19 | centromere regions (hg19) |
| acen_hg38 | centromere regions (hg38) |
| aggregate_counts | Utility function to make reference gene expression profiles |
| analyze_bulk | Call CNVs in a pseudobulk profile using the Numbat joint HMM |
| annot_consensus | Annotate a consensus segments on a pseudobulk dataframe |
| annot_haplo_segs | Annotate haplotype segments after HMM decoding |
| annot_ref | example reference cell annotation |
| annot_segs | Annotate copy number segments after HMM decoding |
| annot_superclones | Annotate superclones on a tree |
| annot_theta_roll | Annotate rolling estimate of imbalance level theta |
| approx_phi_post | Laplace approximation of the posterior of expression fold... |
| approx_theta_post | Laplace approximation of the posterior of allelic imbalance... |
| binary_entropy | calculate entropy for a binary variable |
| bulk_example | example pseudobulk dataframe |
| calc_allele_lik | Calculate allele likelihoods |
| calc_allele_LLR | Calculate LLR for an allele HMM |
| calc_cluster_dist | Calculate expression distance matrix between cell populatoins |
| calc_exp_LLR | Calculate LLR for an expression HMM |
| calc_phi_mle_lnpois | Calculate the MLE of expression fold change phi |
| calc_trans_mat | Calculate the transition matrix for joint HMM |
| check_allele_df | check the format of a allele dataframe |
| check_exp_ref | check the format of lambdas_ref |
| check_matrix | check the format of a count matrix |
| choose_ref_cor | choose beest reference for each cell based on correlation |
| chrom_sizes_hg19 | chromosome sizes (hg19) |
| chrom_sizes_hg38 | chromosome sizes (hg38) |
| classify_alleles | classify alleles using viterbi and forward-backward |
| cnv_heatmap | Plot CNV heatmap |
| combine_bulk | Combine allele and expression pseudobulks |
| compute_posterior | Do bayesian averaging to get posteriors |
| contract_nodes | Merge adjacent set of nodes |
| count_mat_example | example gene expression count matrix |
| count_mat_ref | example reference count matrix |
| dbbinom | Beta-binomial distribution density function A distribution is... |
| detect_clonal_loh | Call clonal LOH using SNP density. Rcommended for cell lines... |
| df_allele_example | example allele count dataframe |
| dpoilog | Returns the density for the Poisson lognormal distribution... |
| expand_states | expand multi-allelic CNVs into separate entries in the... |
| exp_hclust | Run smoothed expression-based hclust |
| fill_neu_segs | Fill neutral regions into consensus segments |
| filter_genes | filter for mutually expressed genes |
| find_common_diploid | Find the common diploid region in a group of pseudobulks |
| fit_bbinom | fit a Beta-Binomial model by maximum likelihood |
| fit_gamma | fit gamma maximum likelihood |
| fit_gpois | fit a Gamma-Poisson model by maximum likelihood |
| fit_lnpois | fit a PLN model by maximum likelihood |
| fit_ref_sse | Fit a reference profile from multiple references using... |
| forward_back_allele | Forward-backward algorithm for allele HMM |
| gaps_hg19 | genome gap regions (hg19) |
| gaps_hg38 | genome gap regions (hg38) |
| genotype | Genotyping main function |
| get_allele_bulk | Aggregate into pseudobulk alelle profile |
| get_allele_hmm | Get an allele HMM |
| get_allele_post | get CNV allele posteriors |
| get_bulk | Aggregate single-cell data into combined bulk expression and... |
| get_clone_post | Map cells to the phylogeny (or genotypes) based on CNV... |
| get_exp_bulk | Aggregate into bulk expression profile |
| get_exp_likelihoods | get the single cell expression likelihoods |
| get_exp_post | compute single-cell expression posteriors |
| get_exp_sc | get the single cell expression dataframe |
| get_haplotype_post | Get phased haplotypes |
| get_internal_nodes | Helper function to get the internal nodes of a dendrogram and... |
| get_joint_post | get joint posteriors |
| get_lambdas_bar | Get average reference expressio profile based on single-cell... |
| get_move_cost | Get the cost of a mutation reassignment |
| get_move_opt | Get the least costly mutation reassignment |
| get_mut_tree | Convert a single-cell phylogeny with mutation placements into... |
| get_nodes_celltree | Get the internal nodes of a dendrogram and the leafs in each... |
| get_segs_consensus | Extract consensus CNV segments |
| get_segs_neu | get neutral segments from multiple pseudobulks |
| get_snps | process VCFs into SNP dataframe |
| get_trans_probs | Helper function to calculate transition porbabilities |
| get_tree_post | Find maximum lilkelihood assignment of mutations on a tree |
| gexp_roll_example | example smoothed gene expression dataframe |
| gtf_hg19 | gene model (hg19) |
| gtf_hg38 | gene model (hg38) |
| hc_example | example hclust tree |
| joint_post_example | example joint single-cell cnv posterior dataframe |
| label_edges | Annotate the direct upstream or downstream mutations on the... |
| label_genotype | Label the genotypes on a mutation graph |
| ladderize | from ape |
| l_bbinom | calculate joint likelihood of allele data |
| l_gpois | calculate joint likelihood of a gamma-poisson model |
| l_lnpois | calculate joint likelihood of a PLN model |
| l_s_v | Compute site branch likelihood (not used) |
| make_group_bulks | Make a group of pseudobulks |
| mark_tumor_lineage | Mark the tumor lineage of a phylogeny |
| Modes | Get the modes of a vector |
| mut_graph_example | example mutation graph |
| mut_to_tree | Transfer mutation assignment onto a single-cell phylogeny |
| nni | Generate tree neighbourhood |
| nnin | Perform the NNI at a specific branch |
| Numbat | Numbat R6 class |
| perform_nni | Maximum likelihood tree search via NNI |
| phi_hat_roll | Rolling estimate of expression fold change phi |
| phi_hat_seg | Estimate of expression fold change phi in a segment |
| phylogeny_example | example single-cell phylogeny |
| plot_bulks | Plot a group of pseudobulks HMM profile |
| 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 |
| pnorm.range.log | Get the total probability from a region of a normal pdf |
| pre_likelihood_hmm | HMM object for unit tests |
| preprocess_allele | Preprocess allele data |
| ref_hca | reference expression magnitudes from HCA |
| ref_hca_counts | reference expression counts from HCA |
| resolve_cnvs | Get unique CNVs from set of segments |
| retest_bulks | retest consensus segments on pseudobulks |
| retest_cnv | retest CNVs in a pseudobulk |
| run_allele_hmm | allele-only HMM |
| run_group_hmms | Run multiple HMMs |
| run_joint_hmm | Run joint HMM on a pseudobulk profile |
| run_numbat | Run workflow to decompose tumor subclones |
| score_mut | Score mutations on goodness of fit on the tree |
| score_mut_helper | Helper for mutation scoring |
| score_tree | score a tree based on maximum likelihood |
| segs_example | example CNV segments dataframe |
| simes_p | Calculate simes' p |
| simplify_history | Simplify the mutational history based on likelihood evidence |
| smooth_expression | filtering, normalization and capping |
| smooth_segs | Smooth the segments after HMM decoding |
| switch_prob_cm | predict phase switch probablity as a function of genetic... |
| test_multi_allelic | test for multi-allelic CNVs |
| theta_hat_roll | Rolling estimate of imbalance level theta |
| theta_hat_seg | Estimate of imbalance level theta in a segment |
| to_phylo | Convert the phylogeny from tidygraph to igraph object |
| transfer_links | Annotate the direct upstream or downstream node on the edges |
| upgma | UPGMA and WPGMA clustering |
| vcf_meta | example VCF header |
| viterbi_allele | Viterbi algorithm for allele HMM |
| viterbi_joint | Generalized viterbi algorithm for joint HMM |
| viterbi_loh | Viterbi for clonal LOH detection |
