Preprocessing and Analysis of Deep Mutational Scanning Data

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Documentation for package ‘mutscan’ version 0.99.2

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

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