a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.

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Documentation for package ‘DEqMS’ version 1.25.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

equalMedianNormalization	normalize to have equal medians in all samples
medianSummary	summarize peptide/PSM intensity into protein level relative abundance estimate by taking the median
medianSweeping	summarize peptide/PSM intensity into protein level relative abundance estimate by median sweeping method
medpolishSummary	summarize peptide/PSM intensity into protein level relative abundance estimate by Turkey median polish procedure
outputResult	output the DEqMS analysis results in a data frame
peptideProfilePlot	plot log2 intensities of all peptides for one gene in different samples
Residualplot	plot the residuals against the number of quantified peptides/PSMs.
spectraCounteBayes	Peptide/Spectra Count Based Empirical Bayes Statistics for Differential Expression
VarianceBoxplot	generate a boxplot of the variance
VarianceScatterplot	generate a scatter plot of the variance