qPLEXanalyzer-package {qPLEXanalyzer} | R Documentation |
Tools for quantitiative proteomics data analysis generated from qPLEX-RIME method
Package: | qPLEXanalyzer |
Type: | Package |
Version: | 1.0.0 |
Date: | 2018-04-23 |
License: | GPL |
Depends: | methods |
The package offers the following functionalities
Data processing, normalization & analysis:
convertToMSnset: Converts quantitative data to a MSnSet
summarizeIntensities: Summarizes multiple peptide measurements for a protein
normalizeQuantiles: Performs quantile normalization on the peptides/proteins intensities
normalizeScaling: Performs scaling normalization on the peptides/proteins intensities (mean, median or sum)
groupScaling: Performs scaling normalization on the peptides/proteins intensities within group (median or mean)
rowScaling: Normalization by scaling peptide/protein intensity across all samples
regressIntensity: Performs linear regression on protein intensities based on selected protein
computeDiffStats: Compute differential statistics for the given contrasts
getContrastResults: Get differential statistics results for given contrast
Visualization:
assignColours: Assigns colours to samples in groups
intensityPlot: Intensity distribution plot of all the samples
intensityBoxplot: Intensity distribution boxplot of all the samples
peptideIntensityPlot: Peptide intensity distribution plot of specific protein
pcaPlot: PCA plot of all the samples
maVolPlot: MA or Volcano plot of differential analysis results
corrPlot: Correlation plot of all the samples
rliPlot: Relative intensity plot of all the samples
hierarchicalPlot: Hierarchical clustering plot of all the samples
plotMeanVar: Computes and plots mean-variance for samples in MSnSet
coveragePlot: Computes and display protein sequence coverage of selected protein in proteomics experiment
Matthew Eldridge, Kamal Kishore, Ashley Sawle (Maintainer)