Package index • 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