Man pages for hahmmr
Haplotype-Aware Hidden Markov Model for RNA
| acen_hg19 | centromere regions (hg19) |
| acen_hg38 | centromere regions (hg38) |
| analyze_allele | Analyze allele profile |
| analyze_joint | Analyze allele and expression profile |
| annot_cm | Annotate genetic distance between markers |
| annot_segs | Annotate copy number segments after HMM decoding |
| approx_phi_post | Laplace approximation of the posterior of expression fold... |
| approx_theta_post_s2 | Find optimal theta of a CNV segment using forward-backward;... |
| approx_theta_post_s3 | Find optimal theta of a chromosome using forward-backward;... |
| bulk_example | example pseudobulk dataframe |
| calc_allele_lik_s2 | Calculate allele likelihoods for 2-state allele HMM |
| calc_allele_lik_s3 | Calculate allele likelihoods for 3-state allele HMM |
| calc_allele_LLR | Calculate LLR for an allele HMM |
| calc_exp_LLR | Calculate LLR for an expression HMM |
| calc_trans_mat_s15 | Calculate the transition matrix for 15-state joint HMM |
| calc_trans_mat_s7 | Calculate the transition matrix for 7-state joint HMM |
| check_cols | Check if columns are present in dataframe |
| check_matrix | Check the format of a count matrix |
| chrom_sizes_hg19 | chromosome sizes (hg19) |
| chrom_sizes_hg38 | chromosome sizes (hg38) |
| classify_alleles | classify alleles using viterbi and forward-backward |
| combine_bulk | Combine allele and expression pseudobulks |
| dbbinom | Beta-binomial distribution density function A distribution is... |
| df_allele_example | example allele count dataframe |
| dpoilog | Returns the density for the Poisson lognormal distribution... |
| filter_genes | filter for mutually expressed genes |
| fit_gamma | fit gamma maximum likelihood |
| fit_lnpois_cpp | Fit MLE of log-normal Poisson model |
| 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) |
| gene_counts_example | example gene expression counts matrix |
| generate_postfix | Generate alphabetical postfixes |
| get_allele_bulk | Aggregate into pseudobulk alelle profile |
| get_allele_hmm_s2 | Make a 2-state allele HMM - no transitions to netural state |
| get_allele_hmm_s3 | Make a 3-state allele HMM - allow transitions to netural... |
| get_bulk | Produce combined bulk expression and allele profile |
| get_exp_bulk | Aggregate into bulk expression profile |
| get_trans_probs_s15 | Helper function to calculate transition porbabilities for... |
| get_trans_probs_s7 | Helper function to calculate transition porbabilities for... |
| gtf_hg19 | gene model (hg19) |
| gtf_hg38 | gene model (hg38) |
| gtf_mm10 | gene model (mm10) |
| l_bbinom | calculate joint likelihood of allele data |
| likelihood_allele | Only compute total log likelihood from an allele HMM |
| l_lnpois | calculate joint likelihood of a PLN model |
| logSumExp | logSumExp function |
| plot_bulks | Plot a group of pseudobulk HMM profiles |
| plot_psbulk | Plot a pseudobulk HMM profile |
| pre_likelihood_hmm | HMM object for unit tests |
| ref_hca | reference expression magnitudes from HCA |
| ref_hca_counts | reference expression counts from HCA |
| run_allele_hmm_s3 | Run a 3-state allele HMM |
| run_allele_hmm_s5 | Run a 5-state allele-only HMM - two theta levels |
| run_joint_hmm_s15 | Run 15-state joint HMM on a pseudobulk profile |
| run_joint_hmm_s7 | Run 7-state joint HMM on a pseudobulk profile |
| segs_example | example CNV segments dataframe |
| smooth_segs | Smooth the segments after HMM decoding |
| switch_prob_cm | predict phase switch probablity as a function of genetic... |
| theta_hat_seg | Estimate of imbalance level theta in a segment |
| vcf_meta | example VCF header |
| viterbi_allele | Viterbi algorithm for allele HMM |
| viterbi_joint | Viterbi algorithm for joint HMM, can only handle one set of... |
| viterbi_joint_mat | Generalized viterbi algorithm for joint HMM, can handle... |
