Haplotype-Aware Hidden Markov Model for RNA

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Documentation for package ‘hahmmr’ version 1.0.0

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acen_hg19 centromere regions (hg19)
acen_hg38 centromere regions (hg38)
analyze_allele Analyze allele profile
analyze_joint Analyze allele and expression profile
bulk_example example pseudobulk dataframe
chrom_sizes_hg19 chromosome sizes (hg19)
chrom_sizes_hg38 chromosome sizes (hg38)
dbbinom Beta-binomial distribution density function A distribution is beta-binomial if p, the probability of success, in a binomial distribution has a beta distribution with shape parameters alpha > 0 and beta > 0 For more details, see extraDistr::dbbinom
df_allele_example example allele count dataframe
dpoilog Returns the density for the Poisson lognormal distribution with parameters mu and sig
fit_lnpois_cpp Fit MLE of log-normal Poisson model
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
get_allele_bulk Aggregate into pseudobulk alelle profile
get_bulk Produce combined bulk expression and allele profile
gtf_hg19 gene model (hg19)
gtf_hg38 gene model (hg38)
gtf_mm10 gene model (mm10)
likelihood_allele Only compute total log likelihood from an allele HMM
logSumExp logSumExp function
l_bbinom calculate joint likelihood of allele data
l_lnpois calculate joint likelihood of a PLN model
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_s5 Run a 5-state allele-only HMM - two theta levels
run_joint_hmm_s15 Run 15-state joint HMM on a pseudobulk profile
segs_example example CNV segments dataframe
vcf_meta example VCF header