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)
l_bbinom                calculate joint likelihood of allele data
l_lnpois                calculate joint likelihood of a PLN model
likelihood_allele       Only compute total log likelihood from an
                        allele HMM
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_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
