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 |