Package index • PhosR

All functions
`KinaseFamily`	KinaseFamily
`UniprotID()` `UniprotID<-`() `GeneSymbol()` `GeneSymbol<-`() `Site()` `Site<-`() `Residue()` `Residue<-`() `Sequence()` `Sequence<-`() `Localisation()` `Localisation<-`()	PhosphoExperiment object accessors
`[`(<PhosphoExperiment>,<ANY>,<ANY>,<ANY>) `[<-`(<PhosphoExperiment>,<ANY>,<ANY>,<ANY>) `rbind(<PhosphoExperiment>)` `cbind(<PhosphoExperiment>)`	PhosphoExperiment object subset, combine methods
`PhosphoExperiment()`	The PhosphoExperiment class
`PhosphoSitePlus`	PhosphoSitePlus annotations for human
`PhosphoSitePlus`	PhosphoSitePlus annotations for mouse
`PhosphoSitePlus`	PhosphoSitePlus annotations for rat
`RUVphospho()`	RUV for phosphoproteomics data normalisation
`SPSs`	A list of Stably Phosphorylated Sites (SPSs)
`Signalomes()`	PhosR Signalomes
`createFrequencyMat()`	Create frequency matrix
`frequencyScoring()`	Frequency scoring
`getSPS()`	Generate set of stable phosphoporylated sites
`SEGs`	A list of Stably Expressed Genes (SEGs)
`kinaseSubstrateHeatmap()`	Kinase-substrate annotation prioritisation heatmap
`kinaseSubstratePred()`	kinaseSubstratePred
`kinaseSubstrateProfile()`	Kinase substrate profiling
`kinaseSubstrateScore()`	Kinase substrate scoring
`mIntersect()` `mUnion()`	Multi-intersection, union
`SEGs`	A list of Stably Expressed Genes (SEGs)
`matANOVA()`	ANOVA test
`meanAbundance()`	Obtain average expression from replicates
`medianScaling()`	Median centering and scaling
`minmax()`	Minmax scaling
`KinaseMotifs`	List of human kinase motifs
`KinaseMotifs`	List of mouse kinase motifs
`KinaseMotifs`	List of rat kinase motifs
`pathwayOverrepresent()`	phosphosite/Gene set over-representation analysis
`pathwayRankBasedEnrichment()`	Phosphosite/Gene set enrichment analysis
`phosCollapse()`	Summarising phosphosites to proteins
`phospho_L6_ratio`	phospho.L6.ratio
`phospho_L6_ratio_pe`	phospho_L6_ratio_pe
`phospho.cells.Ins.sample` `phospho.cells.Ins.pe`	phospho.cells.Ins
`phospho_liverInsTC_RUV_sample`	phospho_liverInsTC_RUV_sample
`phospho.liver.Ins.TC.ratio.RUV.pe`	phospho.liver.Ins.TC.ratio.RUV.pe
`plotKinaseNetwork()`	Plot kinase network
`plotQC()`	A set of function for data QC plot
`plotSignalomeMap()`	Plot signalome map
`ptImpute()`	Paired-tail (pt) based impute
`scImpute()`	Site- and condition-specific (sc) impute
`selectGrps()`	Select by treatment groups (replicate block)
`selectLocalisedSites()`	Select phosphosites by localisation score
`selectOverallPercent()`	Select phosphosite by percentage of quantification
`selectTimes()`	selectTimes
`siteAnnotate()`	Phosphosite annotation
`standardise()`	Standardisation
`tImpute()`	Tail-based impute

Reference

All functions