ConcordanceRule         Create a ConcordanceRule object
ConcordanceRule-class   ConcordanceRule: agreement required between
                        technical replicates
ISNVFilter              Create an ISNVFilter object
ISNVFilter-class        ISNVFilter: Quality control filter for iSNV
                        analysis
WHE-combine             Combine WithinHostExperiment objects by rows or
                        columns
WithinHostExperiment    Create a WithinHostExperiment from components
WithinHostExperiment-class
                        WithinHostExperiment: Container for within-host
                        pathogen variant data
WithinHostExperiment-package
                        WithinHostExperiment: Within-Host Pathogen
                        Variant QC, Diversity, and Bottleneck
WithinHostSFS-class     WithinHostSFS: Site Frequency Spectrum for
                        within-host variants
adaptiveFilter          Create a technology-appropriate ISNVFilter
annotateCodonChange     Codon and amino acid consequence of each SNV
annotateGenes           Label variant sites with the genes they overlap
asViralBottleneckInput
                        Export data for ViralBottleneck package
benchmarkCallers        Benchmark variant callers against truth or each
                        other
buildSFS                Build a site frequency spectrum from a
                        WithinHostExperiment
buildSFSList            Build SFS for all samples in a
                        WithinHostExperiment
calcCallerConcordance   Pairwise caller concordance matrix
calcDiversity           Compute within-host diversity indices
calcNeutralityTests     Compute neutrality test statistics
calcSharedVariants      Calculate shared variant statistics
chao1ISNV               Chao1 richness estimator for iSNV data
checkDiversityPlausibility
                        Check diversity estimates against heuristic
                        plausibility ranges
coerce-WHE              Convert between WithinHostExperiment,
                        data.frame, VRanges and VCF
compareDiversity        Compare diversity between sample groups
compareSFS              Compare two within-host SFS objects
consensusISNV           Multi-caller consensus iSNV detection
consensusSequences      Consensus sequence of each sample
correctSFSBias          Correct ascertainment bias in the within-host
                        SFS
detectCrossContamination
                        Detect potential cross-contamination between
                        samples
detectEmergingVariants
                        Detect emerging variants across time points
estimateSelectionCoefficient
                        Estimate selection coefficient from frequency
                        trajectory
exactBottleneck         Exact bottleneck size estimation
example_whe             Example WithinHostExperiment dataset
exportPairFrequencies   Export donor-recipient frequency table
fitDiversityModel       Fit a linear model to diversity data
flagISNV                Flag iSNV sites based on quality criteria
flagPrimerSites         Flag iSNVs in primer binding regions
flagReplicateDiscordance
                        Flag iSNVs with replicate discordance
flagStrandBiasSCI       Flag strand-biased iSNVs using the SCI metric
flagTemporalInconsistency
                        Flag temporally inconsistent iSNVs in
                        longitudinal data
fusFs                   Fu's Fs statistic
multitestCorrection     Multiple testing correction for p-values
neutralityFromSFS       Compute all neutrality statistics from a
                        WithinHostSFS
pNpSWithinHost          Within-host pN/pS ratio
permutationTest         Permutation test for two-group comparison
piISNV                  Nucleotide diversity (pi) from iSNV frequencies
plotFrequencySpectrum   Plot iSNV frequency spectrum
plotFrequencyTrajectory
                        Plot allele frequency trajectories over time
plotPairScatter         Plot donor-recipient frequency scatter
plotQCDashboard         QC dashboard plot
plotSFS                 Plot a within-host site frequency spectrum
qcLog                   Access the QC audit log
qcSummary               Generate a QC summary report
quickBottleneck         Quick bottleneck size estimation (beta-binomial
                        approximate MLE)
readWithinHost          Import iSNV data from VCF files
readWithinHostTable     Import iSNV data from tabular files
sciStrandBias           Strand Coverage Imbalance (SCI) score
shannonISNV             Shannon entropy from iSNV frequencies
simpsonISNV             Simpson diversity index for iSNV frequencies
tajimaD                 Tajima's D statistic
trackFrequency          Track variant frequency trajectories over time
wattersonISNV           Watterson's theta from iSNV count
