Within-Host Pathogen Variant QC, Diversity, and Bottleneck

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Documentation for package ‘WithinHostExperiment’ version 0.99.2

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

WithinHostExperiment-package	WithinHostExperiment: Within-Host Pathogen Variant QC, Diversity, and Bottleneck
.ConcordanceRule	ConcordanceRule: agreement required between technical replicates
.ISNVFilter	ISNVFilter: Quality control filter for iSNV analysis
.WithinHostExperiment	WithinHostExperiment: Container for within-host pathogen variant data
.WithinHostSFS	WithinHostSFS: Site Frequency Spectrum for within-host variants
adaptiveFilter	Create a technology-appropriate ISNVFilter
annotateCodonChange	Codon and amino acid consequence of each SNV
annotateCodonChange-method	Codon and amino acid consequence of each SNV
annotateGenes	Label variant sites with the genes they overlap
annotateGenes-method	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
calcDiversity-method	Compute within-host diversity indices
calcNeutralityTests	Compute neutrality test statistics
calcNeutralityTests-method	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-method	Convert between WithinHostExperiment, data.frame, VRanges and VCF
coerce-WHE	Convert between WithinHostExperiment, data.frame, VRanges and VCF
combineCols-method	Combine WithinHostExperiment objects by rows or columns
combineRows-method	Combine WithinHostExperiment objects by rows or columns
compareDiversity	Compare diversity between sample groups
compareSFS	Compare two within-host SFS objects
ConcordanceRule	Create a ConcordanceRule object
ConcordanceRule-class	ConcordanceRule: agreement required between technical replicates
consensusISNV	Multi-caller consensus iSNV detection
consensusSequences	Consensus sequence of each sample
consensusSequences-method	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
flagISNV-method	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
ISNVFilter	Create an ISNVFilter object
ISNVFilter-class	ISNVFilter: Quality control filter for iSNV analysis
multitestCorrection	Multiple testing correction for p-values
neutralityFromSFS	Compute all neutrality statistics from a WithinHostSFS
passedISNV	Access the QC audit log
passedISNV-method	Access the QC audit log
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
pNpSWithinHost	Within-host pN/pS ratio
pNpSWithinHost-method	Within-host pN/pS ratio
qcFilters	Access the QC audit log
qcFilters-method	Access the QC audit log
qcFilters<-	Access the QC audit log
qcFilters<--method	Access the QC audit log
qcLog	Access the QC audit log
qcLog-method	Access the QC audit log
qcLog<-	Access the QC audit log
qcLog<--method	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
show-method	ConcordanceRule: agreement required between technical replicates
show-method	ISNVFilter: Quality control filter for iSNV analysis
show-method	WithinHostExperiment: Container for within-host pathogen variant data
show-method	WithinHostSFS: Site Frequency Spectrum for within-host variants
simpsonISNV	Simpson diversity index for iSNV frequencies
tajimaD	Tajima's D statistic
trackFrequency	Track variant frequency trajectories over time
transmissionPairs	Access the QC audit log
transmissionPairs-method	Access the QC audit log
wattersonISNV	Watterson's theta from iSNV count
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
WithinHostSFS	WithinHostSFS: Site Frequency Spectrum for within-host variants
WithinHostSFS-class	WithinHostSFS: Site Frequency Spectrum for within-host variants
[-method	WithinHostExperiment: Container for within-host pathogen variant data