Package: WithinHostExperiment 0.99.2

Introduction | What an iSNV is | What this package is for | What this package does not do | Relationship to existing tools | Why Bioconductor | A warning about the example numbers | Installation | The WithinHostExperiment object | The standard assays | The row ranges | The sample table | The first added slot: qcLog | The second added slot: qcFilters | What subsetting and combining do to the two slots | What the validity method enforces | Converting to other containers | Importing calls | From VCF files | From a VCF already read into R | From an iVar table | Quality control | Describing a filter | Applying a filter | Summarising quality per sample | Extracting the calls that passed | Technology-specific defaults | Replicate-aware quality control | Masking primer sites | Strand bias | Detecting cross-contamination | Putting the steps together | Annotation | Labelling sites with genes | Codon and amino acid consequences | Diversity | How much variation a host carries | Checking an estimate for plausibility | Modelling diversity across samples | Site frequency spectrum | Building a spectrum | Correcting for what could not be seen | Comparing two spectra | Neutrality and selection | Neutrality statistics from the object | Statistics from a spectrum, including Fay and Wu's H | Within-host pN/pS | Consensus sequences for between-host comparison | Selection coefficients from a trajectory | Transmission | Finding the pairs | Counting shared variants | A quick bottleneck estimate | Estimators that model depth | Exporting for other tools | Longitudinal data | Tracking frequencies over time | Detecting emerging variants | Flagging temporally inconsistent sites | Several callers | Building a consensus call set | Measuring agreement between callers | Statistics | Visualisation | The frequency spectrum of an object | Donor against recipient | A quality-control dashboard | A spectrum object | A trajectory | A worked example on real data | The data | Recording the genome length | Quality control and diversity | Checking the magnitudes | Other pathogens | Influenza A | HIV-1 | Mycobacterium tuberculosis | Neutrality statistics across the three | Scope and limitations | Glossary | References | Session information