# Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies

## Documentation for package ‘Rariant’ version 1.22.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

Rariant-package | Rariant package
acCi | Confidence Interval Functions
baseFillScale | Rariant color scales
callConsensus | Tally processing low-level functions
ciAdjustLevel | CI Adjust
ciCovers | CI Utils
ciOutside | CI Utils
ciOverlap | CI Utils
ciWidth | CI Utils
coverageProbability | Assessment of CI methods
eventFillScale | Rariant color scales
evidenceHeatmap | Variant Evidence Heatmap
feTest | Testing Functions
filterCalls | Multi call processing
findCalls | Multi call processing
gr2pos | Position converters
mergeCalls | Multi call processing
mismatchCount | Tally processing low-level functions
mismatchUtils | Tally processing low-level functions
nhsCi | Confidence Interval Functions
nmTest | Testing Functions
plotAbundanceShift | Plotting Functions
plotCIs | Plotting Functions
plotConfidenceIntervals | Plotting Functions
pos2gr | Position converters
propCIs | Confidence Interval Functions
propTests | Testing Functions
Rariant | Rariant package
rariant | Rariant calling functions
rariant-method | Rariant calling functions
rariant-methods | Rariant calling functions
rariantInspect | Interactive inspection
rariantStandalone | Rariant calling functions
rateFillScale | Rariant color scales
readRariant | Rariant calling functions
scoreTest | Testing Functions
selectStrand | Tally processing low-level functions
seqDepth | Tally processing low-level functions
splitSample | Split Sample for Binomial Data
splitSampleBinom | Split Sample for Binomial Data
tallyBamRegion | Tally a genomic region
tallyPlot | Mismatch plot from BAM files
updateCalls | Multi call processing
verdictColorScale | Rariant color scales
writeRariant | Rariant calling functions
yesNoMaybe | Determine Variant Evidence