Package index • DEprot

All functions
`DEprot-class`	DEprot class
`DEprot-dollar-methods` `$,DEprot-method` `$<-,DEprot-method` `$,DEprot.analyses-method` `$<-,DEprot.analyses-method` `$,DEprot.PCA-method` `$<-,DEprot.PCA-method` `$,DEprot.PCoA-method` `$<-,DEprot.PCoA-method` `$,DEprot.correlation-method` `$<-,DEprot.correlation-method` `$,DEprot.upset-method` `$<-,DEprot.upset-method` `$,DEprot.contrast.heatmap-method` `$<-,DEprot.contrast.heatmap-method` `$,DEprot.counts.heatmap-method` `$<-,DEprot.counts.heatmap-method` `$,DEprot.enrichResult-method` `$<-,DEprot.enrichResult-method` `$,DEprot.pvalues-method` `$<-,DEprot.pvalues-method` `$,DEprot.normality-method` `$<-,DEprot.normality-method` `$,DEprot.RMSE-method` `$<-,DEprot.RMSE-method` `$,DEprot.SAINTq-method` `$<-,DEprot.SAINTq-method` `$,DEprot.missingness-method` `$<-,DEprot.missingness-method` `$,DEprot.outliers-method` `$<-,DEprot.outliers-method` `$,DEprot.power-method` `$<-,DEprot.power-method` `$,DEprot.sPLSDA-method` `$<-,DEprot.sPLSDA-method` `$,DEprot.timecourse-method` `$<-,DEprot.timecourse-method` `$,DEprot.timecourse.enrichment-method` `$<-,DEprot.timecourse.enrichment-method`	Slot access for DEprot classes
`DEprot.PCA-class`	DEprot.PCA class
`DEprot.PCoA-class`	DEprot.PCoA class
`DEprot.RMSE-class`	DEprot.RMSE class
`DEprot.SAINTq-class`	DEprot.SAINTq 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.missingness-class`	DEprot.missingness class
`DEprot.normality-class`	DEprot.normality class
`DEprot.outliers-class`	DEprot.outliers class
`DEprot.power-class`	DEprot.power class
`DEprot.pvalues-class`	DEprot.pvalues class
`DEprot.sPLSDA-class`	DEprot.sPLSDA class
`DEprot.timecourse-class`	DEprot.timecourse class
`DEprot.timecourse.enrichment-class`	DEprot.timecourse.enrichment class
`DEprot.upset-class`	DEprot.upset class
`NES.plot()`	NES.plot
`SAINTq()`	SAINTq
`add.protein.info()`	add.protein.info
`affinity.propagation()`	affinity.propagation
`analyze.timecourse()`	analyze.timecourse
`as.MSnSet()`	as.MSnSet
`as.QFeatures()`	as.QFeatures
`as.SummarizedExperiment()`	as.SummarizedExperiment
`check.normality()`	check.normality
`check.pvalues()`	check.pvalues
`combine.enrichments()`	combine.enrichments
`compare(<imp.methods>)`	compare.imp.methods
`compare(<ranking>)`	compare.ranking
`contrast.LFQ()`	contrast.LFQ
`contrast.scatter()`	contrast.scatter
`corum_v4.1`	CORUM version 4.1
`corum_v5.0`	CORUM version 5.0
`detect.outliers()`	detect.outliers
`diff(<analyses>)`	diff.analyses
`diff(<analyses.limma>)`	diff.analyses.limma
`diff(<analyses.proDA>)`	diff.analyses.proDA
`diff(<analyses.prolfqua>)`	diff.analyses.prolfqua
`divergent.enrichment()`	divergent.enrichment
`dpo.imputed.counts`	Imputed proteomics (LFQ) data
`estimate.power()`	estimate.power
`export.analyses()`	export.analyses
`export.external()`	export.external
`export.report()`	export.report
`expression.boxplot()`	expression.boxplot
`filter(<proteins>)`	filter.proteins
`filter(<samples>)`	filter.samples
`generate(<mm>)`	generate.mm
`geneset.enrichment()`	geneset.enrichment
`get.metadata()`	get.metadata
`get.protein.info()`	get.protein.info
`get.results()`	get.results
`get.sPLSDA.proteins()`	get.sPLSDA.proteins
`get.sPLSDA.ranking()`	get.sPLSDA.ranking
`get.sPLSDA.results()`	get.sPLSDA.results
`get.timecourse.results()`	get.timecourse.results
`harmonize.batches()`	harmonize.batches
`heatmap.contrasts()`	heatmap.contrasts
`heatmap.counts()`	heatmap.counts
`heatmap.counts.anno()`	heatmap.counts.anno
`heatmap.timecourse()`	heatmap.timecourse
`identify(<distribution>)`	identify.distribution
`import.external()`	import.external
`import.msstats()`	import.msstats
`impute.counts()`	impute.counts
`jaccardSim()`	jaccardSim
`load.counts2()`	load.counts2
`missingness.diagnostic()`	missingness.diagnostic
`normalize.counts()`	normalize.counts
`perform.PCA()`	perform.PCA
`perform.PCoA()`	perform.PCoA
`perform.sPLSDA()`	perform.sPLSDA
`plot(<DEprot.power>,<ANY>)`	DEprot.power plot-method
`plot(<DEprot.timecourse>,<ANY>)`	DEprot.timecourse plot-method
`plot(<DEprot.timecourse.enrichment>,<ANY>)`	DEprot.timecourse.enrichment plot-method
`plot(<GSEA>)`	plot.GSEA
`plot(<MA>)`	plot.MA
`plot(<PC.biplot>)`	plot.PC.biplot
`plot(<PC.cumulative>)`	plot.PC.cumulative
`plot(<PC.scatter.123>)`	plot.PC.scatter.123
`plot(<PC.scatter>)`	plot.PC.scatter
`plot(<PCoA.biplot>)`	plot.PCoA.biplot
`plot(<PCoA.cumulative>)`	plot.PCoA.cumulative
`plot(<PCoA.scatter.123>)`	plot.PCoA.scatter.123
`plot(<PCoA.scatter>)`	plot.PCoA.scatter
`plot(<correlation.heatmap>)`	plot.correlation.heatmap
`plot(<counts>)`	plot.counts
`plot(<sPLSDA.auroc>)`	plot.sPLSDA.auroc
`plot(<sPLSDA.biplot>)`	plot.sPLSDA.biplot
`plot(<sPLSDA.cumulative>)`	plot.sPLSDA.cumulative
`plot(<sPLSDA.loadings>)`	plot.sPLSDA.loadings
`plot(<sPLSDA.performance>)`	plot.sPLSDA.performance
`plot(<sPLSDA.scatter.123>)`	plot.sPLSDA.scatter.123
`plot(<sPLSDA.scatter>)`	plot.sPLSDA.scatter
`plot(<sPLSDA.stability>)`	plot.sPLSDA.stability
`plot(<sPLSDA.tuning>)`	plot.sPLSDA.tuning
`plot(<timecourse.profiles>)`	plot.timecourse.profiles
`plot(<timecourse.protein>)`	plot.timecourse.protein
`plot(<upset>)`	plot.upset
`plot(<volcano>)`	plot.volcano
`protein.summary()`	protein.summary
`randomize.missing.values()`	randomize.missing.values
`rank.timecourse()`	rank.timecourse
`reapply.thresholds()`	reapply.thresholds
`remove.undetected.proteins()`	remove.undetected.proteins
`rename(<samples>)`	rename.samples
`rescale.bait()`	rescale.bait
`rime.dpo`	Imputed RIME (LFQ) data
`rime.saintq`	SAINTq results for RIME
`sPLSDA.enrichment()`	sPLSDA.enrichment
`sample.config`	Example of metadata table
`show(<DEprot>)`	DEprot show-method
`show(<DEprot.PCA>)`	DEprot.PCA show-method
`show(<DEprot.PCoA>)`	DEprot.PCoA show-method
`show(<DEprot.RMSE>)`	DEprot.RMSE show-method
`show(<DEprot.SAINTq>)`	DEprot.SAINTq 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.missingness>)`	DEprot.missingness show-method
`show(<DEprot.normality>)`	DEprot.normality show-method
`show(<DEprot.outliers>)`	DEprot.outliers show-method
`show(<DEprot.power>)`	DEprot.power show-method
`show(<DEprot.pvalues>)`	DEprot.pvalues show-method
`show(<DEprot.sPLSDA>)`	DEprot.sPLSDA show-method
`show(<DEprot.timecourse>)`	DEprot.timecourse show-method
`show(<DEprot.timecourse.enrichment>)`	DEprot.timecourse.enrichment show-method
`show(<DEprot.upset>)`	DEprot.upset show-method
`simplify.enrichment()`	simplify.enrichment
`summary(<DEprot.RMSE>)`	DEprot.RMSE summary-method
`summary(<DEprot.SAINTq>)`	DEprot.SAINTq summary-method
`summary(<DEprot.analyses>)`	DEprot.analyses summary-method
`summary(<DEprot.missingness>)`	DEprot.missingness summary-method
`summary(<DEprot.sPLSDA>)`	DEprot.sPLSDA summary-method
`summary(<DEprot.timecourse>)`	DEprot.timecourse summary-method
`test.toolbox`	Test toolbox
`timecourse.enrichment()`	timecourse.enrichment
`unimputed.counts`	Unimputed proteomics (LFQ) data
`updateObject()`	DEprot updateObject-method

Reference

All functions