Preprocessing and Analysis of Deep Mutational Scanning Data


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Documentation for package ‘mutscan’ version 0.99.2

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