qPLEXanalyzer-package: Tools for qPLEX-RIME data analysis

qPLEXanalyzer-packageR Documentation

Tools for qPLEX-RIME data analysis

Description

Tools for quantitiative proteomics data analysis generated from qPLEX-RIME method 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

  • coefVar: Calculating the coefficient of variation by utilizing expression data within individual sample groups

  • computeDiffStats: Compute differential statistics for the given contrasts

  • getContrastResults: Get differential statistics results for given contrast

Visualization:

  • assignColours: Assigns colours to samples in groups

  • corrPlot: Correlation plot of all the samples

  • coveragePlot: Computes and display protein sequence coverage of

  • hierarchicalPlot: Hierarchical clustering plot of all the samples

  • intensityBoxplot: Intensity distribution boxplot of all the samples

  • intensityPlot: Intensity distribution plot of all the samples

  • maVolPlot: MA or Volcano plot of differential analysis results

  • pcaPlot: PCA plot of all the samples

  • peptideIntensityPlot: Peptide intensity distribution plot of specific protein

  • plotMeanVar: Computes and plots mean-variance for samples in MSnSet

  • rliPlot: Relative intensity plot of all the samples selected protein in proteomics experiment

Author(s)

Matthew Eldridge, Kamal Kishore, Ashley Sawle (Maintainer)

ads2202cu@gmail.com

See Also

Useful links:


crukci-bioinformatics/qPLEXanalyzer documentation built on Sept. 24, 2024, 1:13 a.m.