Package index • DEprot

All functions
`DEprot-class`	DEprot class
`DEprot.PCA-class`	DEprot.PCA class
`DEprot.RMSE-class`	DEprot.RMSE class
`DEprot.analyses-class`	DEprot.analyses class
`DEprot.contrast.heatmap-class`	DEprot.contrast.heatmap class
`DEprot.correlation-class`	DEprot.correlation class
`DEprot.counts.heatmap-class`	DEprot.counts.heatmap class
`DEprot.enrichResult-class`	DEprot.enrichResult class
`DEprot.normality-class`	DEprot.normality class
`DEprot.pvalues-class`	DEprot.pvalues class
`DEprot.upset-class`	DEprot.upset class
`NES.plot()`	NES.plot
`affinity.propagation()`	affinity.propagation
`check.normality()`	check.normality
`check.pvalues()`	check.pvalues
`compare(<imp.methods>)`	compare.imp.methods
`compare(<ranking>)`	compare.ranking
`contrast.scatter()`	contrast.scatter
`corum_v4.1`	CORUM version 4.1
`corum_v5.0`	CORUM version 5.0
`diff(<analyses>)`	diff.analyses
`diff(<analyses.limma>)`	diff.analyses.limma
`diff(<analyses.prolfqua>)`	diff.analyses.prolfqua
`dpo.imputed.counts`	Imputed proteomics (LFQ) data
`export.analyses()`	export.analyses
`expression.boxplot()`	expression.boxplot
`filter(<proteins>)`	filter.proteins
`geneset.enrichment()`	geneset.enrichment
`get.metadata()`	get.metadata
`get.results()`	get.results
`harmonize.batches()`	harmonize.batches
`heatmap.contrasts()`	heatmap.contrasts
`heatmap.counts()`	heatmap.counts
`impute.counts()`	impute.counts
`jaccardSim()`	jaccardSim
`load.counts()`	load.counts
`load.counts2()`	load.counts2
`normalize.counts()`	normalize.counts
`perform.PCA()`	perform.PCA
`plot(<GSEA>)`	plot.GSEA
`plot(<MA>)`	plot.MA
`plot(<PC.cumulative>)`	plot.PC.cumulative
`plot(<PC.scatter.123>)`	plot.PC.scatter.123
`plot(<PC.scatter>)`	plot.PC.scatter
`plot(<correlation.heatmap>)`	plot.correlation.heatmap
`plot(<counts>)`	plot.counts
`plot(<upset>)`	plot.upset
`plot(<volcano>)`	plot.volcano
`protein.summary()`	protein.summary
`randomize.missing.values()`	randomize.missing.values
`reapply.thresholds()`	reapply.thresholds
`remove.undetected.proteins()`	remove.undetected.proteins
`rename(<samples>)`	rename.samples
`rescale.bait()`	rescale.bait
`sample.config`	Example of metadata table
`show(<DEprot>)`	DEprot show-method
`show(<DEprot.PCA>)`	DEprot.PCA show-method
`show(<DEprot.RMSE>)`	DEprot.RMSE show-method
`show(<DEprot.analyses>)`	DEprot.analyses show-method
`show(<DEprot.contrast.heatmap>)`	DEprot.contrast.heatmap show-method
`show(<DEprot.correlation>)`	DEprot.correlation show-method
`show(<DEprot.counts.heatmap>)`	DEprot.counts.heatmap show-method
`show(<DEprot.enrichResult>)`	DEprot.enrichResult show-method
`show(<DEprot.normality>)`	DEprot.normality show-method
`show(<DEprot.pvalues>)`	DEprot.pvalues show-method
`show(<DEprot.upset>)`	DEprot.upset show-method
`simplify.enrichment()`	simplify.enrichment
`summary(<DEprot.RMSE>)`	DEprot.RMSE summary-method
`summary(<DEprot.analyses>)`	DEprot.analyses summary-method
`test.toolbox`	Test toolbox
`unimputed.counts`	Unimputed proteomics (LFQ) data

Reference

All functions