Man pages for whtns/numbat
Haplotype-Aware CNV Analysis from scRNA-Seq

acen_hg19centromere regions (hg19)
acen_hg38centromere regions (hg38)
aggregate_countsUtility function to make reference gene expression profiles
analyze_bulkCall CNVs in a pseudobulk profile using the Numbat joint HMM
annot_consensusAnnotate a consensus segments on a pseudobulk dataframe
annot_haplo_segsAnnotate haplotype segments after HMM decoding
annot_refexample reference cell annotation
annot_segsAnnotate copy number segments after HMM decoding
annot_superclonesAnnotate superclones on a tree
annot_theta_rollAnnotate rolling estimate of imbalance level theta
approx_phi_postLaplace approximation of the posterior of expression fold...
approx_theta_postLaplace approximation of the posterior of allelic imbalance...
binary_entropycalculate entropy for a binary variable
bulk_exampleexample pseudobulk dataframe
calc_allele_likCalculate allele likelihoods
calc_allele_LLRCalculate LLR for an allele HMM
calc_cluster_distCalculate expression distance matrix between cell populatoins
calc_exp_LLRCalculate LLR for an expression HMM
calc_phi_mle_lnpoisCalculate the MLE of expression fold change phi
calc_trans_matCalculate the transition matrix for joint HMM
check_allele_dfcheck the format of a allele dataframe
check_exp_refcheck the format of lambdas_ref
check_matrixcheck the format of a count matrix
choose_ref_corchoose beest reference for each cell based on correlation
chrom_sizes_hg19chromosome sizes (hg19)
chrom_sizes_hg38chromosome sizes (hg38)
classify_allelesclassify alleles using viterbi and forward-backward
cnv_heatmapPlot CNV heatmap
combine_bulkCombine allele and expression pseudobulks
compute_posteriorDo bayesian averaging to get posteriors
contract_nodesMerge adjacent set of nodes
count_mat_exampleexample gene expression count matrix
count_mat_refexample reference count matrix
dbbinomBeta-binomial distribution density function A distribution is...
detect_clonal_lohCall clonal LOH using SNP density. Rcommended for cell lines...
df_allele_exampleexample allele count dataframe
dpoilogReturns the density for the Poisson lognormal distribution...
expand_statesexpand multi-allelic CNVs into separate entries in the...
exp_hclustRun smoothed expression-based hclust
fill_neu_segsFill neutral regions into consensus segments
filter_genesfilter for mutually expressed genes
find_common_diploidFind the common diploid region in a group of pseudobulks
fit_bbinomfit a Beta-Binomial model by maximum likelihood
fit_gammafit gamma maximum likelihood
fit_gpoisfit a Gamma-Poisson model by maximum likelihood
fit_lnpoisfit a PLN model by maximum likelihood
fit_ref_sseFit a reference profile from multiple references using...
forward_back_alleleForward-backward algorithm for allele HMM
gaps_hg19genome gap regions (hg19)
gaps_hg38genome gap regions (hg38)
genotypeGenotyping main function
get_allele_bulkAggregate into pseudobulk alelle profile
get_allele_hmmGet an allele HMM
get_allele_postget CNV allele posteriors
get_bulkAggregate single-cell data into combined bulk expression and...
get_clone_postMap cells to the phylogeny (or genotypes) based on CNV...
get_exp_bulkAggregate into bulk expression profile
get_exp_likelihoodsget the single cell expression likelihoods
get_exp_postcompute single-cell expression posteriors
get_exp_scget the single cell expression dataframe
get_haplotype_postGet phased haplotypes
get_internal_nodesHelper function to get the internal nodes of a dendrogram and...
get_joint_postget joint posteriors
get_lambdas_barGet average reference expressio profile based on single-cell...
get_move_costGet the cost of a mutation reassignment
get_move_optGet the least costly mutation reassignment
get_mut_treeConvert a single-cell phylogeny with mutation placements into...
get_nodes_celltreeGet the internal nodes of a dendrogram and the leafs in each...
get_segs_consensusExtract consensus CNV segments
get_segs_neuget neutral segments from multiple pseudobulks
get_snpsprocess VCFs into SNP dataframe
get_trans_probsHelper function to calculate transition porbabilities
get_tree_postFind maximum lilkelihood assignment of mutations on a tree
gexp_roll_exampleexample smoothed gene expression dataframe
gtf_hg19gene model (hg19)
gtf_hg38gene model (hg38)
hc_exampleexample hclust tree
joint_post_exampleexample joint single-cell cnv posterior dataframe
label_edgesAnnotate the direct upstream or downstream mutations on the...
label_genotypeLabel the genotypes on a mutation graph
ladderizefrom ape
l_bbinomcalculate joint likelihood of allele data
l_gpoiscalculate joint likelihood of a gamma-poisson model
l_lnpoiscalculate joint likelihood of a PLN model
l_s_vCompute site branch likelihood (not used)
make_group_bulksMake a group of pseudobulks
mark_tumor_lineageMark the tumor lineage of a phylogeny
ModesGet the modes of a vector
mut_graph_exampleexample mutation graph
mut_to_treeTransfer mutation assignment onto a single-cell phylogeny
nniGenerate tree neighbourhood
nninPerform the NNI at a specific branch
NumbatNumbat R6 class
perform_nniMaximum likelihood tree search via NNI
phi_hat_rollRolling estimate of expression fold change phi
phi_hat_segEstimate of expression fold change phi in a segment
phylogeny_exampleexample single-cell phylogeny
plot_bulksPlot a group of pseudobulks HMM profile
plot_consensusPlot consensus CNVs
plot_exp_rollPlot single-cell smoothed expression magnitude heatmap
plot_mut_historyPlot mutational history
plot_phylo_heatmapPlot single-cell CNV calls along with the clonal phylogeny
plot_psbulkPlot a pseudobulk HMM profile
plot_sc_treePlot single-cell smoothed expression magnitude heatmap
pnorm.range.logGet the total probability from a region of a normal pdf
pre_likelihood_hmmHMM object for unit tests
preprocess_allelePreprocess allele data
ref_hcareference expression magnitudes from HCA
ref_hca_countsreference expression counts from HCA
resolve_cnvsGet unique CNVs from set of segments
retest_bulksretest consensus segments on pseudobulks
retest_cnvretest CNVs in a pseudobulk
run_allele_hmmallele-only HMM
run_group_hmmsRun multiple HMMs
run_joint_hmmRun joint HMM on a pseudobulk profile
run_numbatRun workflow to decompose tumor subclones
score_mutScore mutations on goodness of fit on the tree
score_mut_helperHelper for mutation scoring
score_treescore a tree based on maximum likelihood
segs_exampleexample CNV segments dataframe
simes_pCalculate simes' p
simplify_historySimplify the mutational history based on likelihood evidence
smooth_expressionfiltering, normalization and capping
smooth_segsSmooth the segments after HMM decoding
switch_prob_cmpredict phase switch probablity as a function of genetic...
test_multi_allelictest for multi-allelic CNVs
theta_hat_rollRolling estimate of imbalance level theta
theta_hat_segEstimate of imbalance level theta in a segment
to_phyloConvert the phylogeny from tidygraph to igraph object
transfer_linksAnnotate the direct upstream or downstream node on the edges
upgmaUPGMA and WPGMA clustering
vcf_metaexample VCF header
viterbi_alleleViterbi algorithm for allele HMM
viterbi_jointGeneralized viterbi algorithm for joint HMM
viterbi_lohViterbi for clonal LOH detection
whtns/numbat documentation built on Nov. 8, 2022, 10:48 a.m.