Package: WithinHostExperiment 0.99.0

Cuiwei Gao

WithinHostExperiment: Within-Host Pathogen Variant QC, Diversity, and Bottleneck

Provides a SummarizedExperiment-based container and workflow functions for analysing intra-host single nucleotide variants (iSNV) from pathogen deep sequencing data. Supports replicate-aware quality control with full provenance tracking, multi-caller import harmonisation, within-host diversity quantification, and standardised export to transmission bottleneck estimation tools. Designed as infrastructure that bridges upstream variant callers (iVar, LoFreq, Freebayes) with downstream analysis packages through a common data object with uncertainty-preserving QC.

Authors:Cuiwei Gao [aut, cre]

WithinHostExperiment_0.99.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
WithinHostExperiment/json (API)

# Install 'WithinHostExperiment' in R:

install.packages('WithinHostExperiment', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cuiweig/withinhostexperiment/issues

Datasets:

example_whe - Example WithinHostExperiment dataset

On CRAN:

genetics variantannotation sequencing genomicvariation qualitycontrol variantdetection dataimport longread

3.30 score 60 exports 71 dependencies

Last updated from:28a1a5c5a7. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	205
linux-devel	OK	411
source / vignettes	OK	325
linux-release	OK	401
macos-release	OK	315
macos-oldrel	OK	248
windows-devel	OK	368
windows-release	OK	361
windows-oldrel	OK	328
wasm-release	OK	162

Exports:adaptiveFilter annotateCodonChange annotateFromGFF asViralBottleneckInput benchmarkCallers buildSFS buildSFSList calcCallerConcordance calcDiversity calcNeutralityTests calcSharedVariants chao1ISNV combineCols combineRows compareDiversity compareSFS consensusISNV correctSFSBias detectCrossContamination detectEmergingVariants dndsWithinHost estimateSelectionCoefficient exactBottleneck exportPairFrequencies fitDiversityModel flagISNV flagPrimerSites flagReplicateDiscordance flagStrandBiasSCI flagTemporalInconsistency fusFs ISNVFilter multitestCorrection neutralityFromSFS passedISNV permutationTest piISNV plotFrequencySpectrum plotFrequencyTrajectory plotPairScatter plotQCDashboard plotSFS qcFilters qcFilters<-qcLog qcLog<-qcSummary quickBottleneck readWithinHost readWithinHostTable sciStrandBias shannonISNV show simpsonISNV tajimaD trackFrequency transmissionPairs validateDiversity wattersonISNV WithinHostExperiment

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys UCSC.utils VariantAnnotation vctrs XML XVector yaml

Introduction to WithinHostExperiment

Rendered fromWithinHostExperiment.Rmdusingknitr::rmarkdown

Last update: 2026-09-17
Started: 2026-03-30

Help page	Topics
WithinHostExperiment: Within-Host Pathogen Variant QC, Diversity, and Bottleneck	WithinHostExperiment-package
Create a technology-appropriate ISNVFilter	adaptiveFilter
Annotate codon changes from GFF3 CDS + reference FASTA	annotateCodonChange
Annotate variant sites from a GFF3 gene model	annotateFromGFF
Export data for ViralBottleneck package	asViralBottleneckInput
Benchmark variant callers against truth or each other	benchmarkCallers
Build a site frequency spectrum from a WithinHostExperiment	buildSFS
Build SFS for all samples in a WithinHostExperiment	buildSFSList
Pairwise caller concordance matrix	calcCallerConcordance
Compute within-host diversity indices	calcDiversity calcDiversity,WithinHostExperiment-method
Compute neutrality test statistics	calcNeutralityTests calcNeutralityTests,WithinHostExperiment-method
Calculate shared variant statistics	calcSharedVariants
Chao1 richness estimator for iSNV data	chao1ISNV
Coerce WithinHostExperiment to data.frame or VRanges	coerce,VRanges,WithinHostExperiment-method coerce,WithinHostExperiment,data.frame-method coerce,WithinHostExperiment,VRanges-method coerce-WHE
Compare diversity between sample groups	compareDiversity
Compare two within-host SFS objects	compareSFS
Multi-caller consensus iSNV detection	consensusISNV
Correct ascertainment bias in the within-host SFS	correctSFSBias
Detect potential cross-contamination between samples	detectCrossContamination
Detect emerging variants across time points	detectEmergingVariants
Within-host dN/dS ratio	dndsWithinHost
Estimate selection coefficient from frequency trajectory	estimateSelectionCoefficient
Exact bottleneck size estimation	exactBottleneck
Example WithinHostExperiment dataset	example_whe
Export donor-recipient frequency table	exportPairFrequencies
Fit a linear model to diversity data	fitDiversityModel
Flag iSNV sites based on quality criteria	flagISNV flagISNV,WithinHostExperiment-method
Flag iSNVs in primer binding regions	flagPrimerSites
Flag iSNVs with replicate discordance	flagReplicateDiscordance
Flag strand-biased iSNVs using the SCI metric	flagStrandBiasSCI
Flag temporally inconsistent iSNVs in longitudinal data	flagTemporalInconsistency
Fu's Fs statistic	fusFs
Create an ISNVFilter object	ISNVFilter
ISNVFilter: Quality control filter for iSNV analysis	.ISNVFilter ISNVFilter-class show,ISNVFilter-method
Multiple testing correction for p-values	multitestCorrection
Compute all neutrality statistics from a WithinHostSFS	neutralityFromSFS
Permutation test for two-group comparison	permutationTest
Nucleotide diversity (pi) from iSNV frequencies	piISNV
Plot iSNV frequency spectrum	plotFrequencySpectrum
Plot allele frequency trajectories over time	plotFrequencyTrajectory
Plot donor-recipient frequency scatter	plotPairScatter
QC dashboard plot	plotQCDashboard
Plot a within-host site frequency spectrum	plotSFS
Access the QC audit log	passedISNV passedISNV,WithinHostExperiment-method qcFilters qcFilters,WithinHostExperiment-method qcFilters<- qcFilters<-,WithinHostExperiment-method qcLog qcLog,WithinHostExperiment-method qcLog<- qcLog<-,WithinHostExperiment-method transmissionPairs transmissionPairs,WithinHostExperiment-method
Generate a QC summary report	qcSummary
Quick bottleneck size estimation (beta-binomial approximate MLE)	quickBottleneck
Import iSNV data from VCF files	readWithinHost
Import iSNV data from tabular files	readWithinHostTable
Strand Coverage Imbalance (SCI) score	sciStrandBias
Shannon entropy from iSNV frequencies	shannonISNV
Simpson diversity index for iSNV frequencies	simpsonISNV
Tajima's D statistic	tajimaD
Track variant frequency trajectories over time	trackFrequency
Check diversity estimates against plausibility ranges	validateDiversity
Watterson's theta from iSNV count	wattersonISNV
Combine WithinHostExperiment objects by rows or columns	combineCols,WithinHostExperiment-method combineRows,WithinHostExperiment-method WHE-combine
Create a WithinHostExperiment from components	WithinHostExperiment
WithinHostExperiment: Container for within-host pathogen variant data	.WithinHostExperiment show,WithinHostExperiment-method WithinHostExperiment-class [,WithinHostExperiment,ANY,ANY,ANY-method
WithinHostSFS: Site Frequency Spectrum for within-host variants	.WithinHostSFS show,WithinHostSFS-method WithinHostSFS WithinHostSFS-class

Package: WithinHostExperiment 0.99.0

WithinHostExperiment: Within-Host Pathogen Variant QC, Diversity, and Bottleneck

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