Function reference • APAFunctions

All functions

ANOVA(): Runs an ANOVA and returns Anova.adj and Anova.idx

HClust(): HClust

PCA_calc(): Compute PCA, no plots

PCA_plot(): Generate 2D and 3D PCA plots

applyttest(): An APAF wrapper for t.test() that works for both proteins and peptides

clean(): TO DO: make a clean function that can clean data based on its type. Blank for now --clean argument should have a flag for the search engine used, e.g. MaxQuant or Protein Discoverer. Version numbers matter as well.

createResultsImagexlsx(): Creates an Excel workbook with each image and a description. Doesn't require any arguments -- creating this workbook is self-contained

createResultsxlsx(): Creates an Excel workbook all results. Later it should format based upon experiment. TO DO: parameter values like normalisation etc should be passed in

getUniprotBatch(): Get UniProt annotations

make_CVs(): TO DETERMINE: make_CVs

mergebyUniprot(): Merge the Uniprot annotation with the results

normalise(): Any normalisation of the data matrix applied to APAF data

plotBoxPlots(): Plotting any APAF boxplots. To be done using ggplot, and take in any experiment type

plotClusterDendrogram(): The one function to plot dendrograms. Future: maybe rewrite with ggdendro?

plotClusterProfile(): Plot cluster profile data

plotCorrelationPlots(): Generic correlation plot function

plotErrorBarsLines(): plot error bars with lines included

plotHeatmaps(): Plots a heatmap with either euclidean or cor distance; ANOVA or no ANOVA

plotRelativeDensities(): Plot the relative of ions (provide ion matrix w/ or wo/ normalisation)

plotVolcano(): The Volcano plot function for all APAF scripts

printxlsxDataSheet(): Set openxlsx style for comparisons and ANOVA table

printxlsxInfoSheet(): Print xlsx information sheet

readInputFiles(): Read mass spec input files and design files for analysis and writes outputs to global environment