Function reference • mutscan

All functions
`calcNearestStringDist()`	Calculate distances to the nearest string
`calculateFitnessScore()`	Calculate fitness scores.
`calculateRelativeFC()`	Calculate logFCs relative to WT using edgeR
`collapseMutantsBySimilarity()` `collapseMutantsByAA()` `collapseMutants()`	Collapse mutants by similarity
`digestFastqs()`	Read, filter and digest sequences from fastq file(s).
`generateQCReport()`	Generate QC report
`groupSimilarSequences()`	Create a conversion table for collapsing similar sequences
`linkMultipleVariants()`	Process an experiment with multiple variable sequences
`plotDistributions()`	Plot distribution of observed values
`plotFiltering()`	Visualize the filtering procedure
`plotMeanDiff()`	Construct an MA (mean-difference) plot
`plotPairs()`	Make pairs plot of selected assay from a SummarizedExperiment object
`plotTotals()`	Plot the column totals of a selected assay
`plotVolcano()`	Construct a volcano plot
`relabelMutPositions()`	Relabel the positions of mutations in the designated ID
`summarizeExperiment()`	Summarize and collapse multiple mutational scanning experiments

Reference