# Preprocessing and Analysis of Deep Mutational Scanning Data

## Documentation for package ‘mutscan’ version 1.1.0

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

## Help Pages

calcNearestStringDist | Calculate distances to the nearest string
calculateFitnessScore | Calculate fitness scores.
calculateRelativeFC | Calculate logFCs relative to WT using edgeR
collapseMutants | Collapse mutants by similarity
collapseMutantsByAA | Collapse mutants by similarity
collapseMutantsBySimilarity | 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