A set of methods and tools for comprehensive analysis of phosphoproteomics data

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Documentation for package ‘PhosR’ version 1.18.0

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

Help Pages

cbind	PhosphoExperiment object subset, combine methods
cbind-method	PhosphoExperiment object subset, combine methods
coerce,	The PhosphoExperiment class
createFrequencyMat	Create frequency matrix
frequencyScoring	Frequency scoring
GeneSymbol	PhosphoExperiment object accessors
GeneSymbol-method	PhosphoExperiment object accessors
GeneSymbol<-	PhosphoExperiment object accessors
GeneSymbol<--method	PhosphoExperiment object accessors
getSPS	Generate set of stable phosphoporylated sites
hSEGs	A list of Stably Expressed Genes (SEGs)
KinaseFamily	KinaseFamily
kinaseSubstrateHeatmap	Kinase-substrate annotation prioritisation heatmap
kinaseSubstratePred	kinaseSubstratePred
kinaseSubstrateProfile	Kinase substrate profiling
kinaseSubstrateScore	Kinase substrate scoring
Localisation	PhosphoExperiment object accessors
Localisation-method	PhosphoExperiment object accessors
Localisation<-	PhosphoExperiment object accessors
Localisation<--method	PhosphoExperiment object accessors
matANOVA	ANOVA test
meanAbundance	Obtain average expression from replicates
medianScaling	Median centering and scaling
minmax	Minmax scaling
mIntersect	Multi-intersection, union
motif.human.list	List of human kinase motifs
motif.mouse.list	List of mouse kinase motifs
motif.rat.list	List of rat kinase motifs
mSEGs	A list of Stably Expressed Genes (SEGs)
mUnion	Multi-intersection, union
pathwayOverrepresent	phosphosite/Gene set over-representation analysis
pathwayRankBasedEnrichment	Phosphosite/Gene set enrichment analysis
phosCollapse	Summarising phosphosites to proteins
phospho.cells.Ins	phospho.cells.Ins
phospho.cells.Ins.pe	phospho.cells.Ins
phospho.L6.ratio	phospho.L6.ratio
phospho.L6.ratio.pe	phospho_L6_ratio_pe
phospho.liver.Ins.TC.ratio.RUV	phospho_liverInsTC_RUV_sample
phospho.liver.Ins.TC.ratio.RUV.pe	phospho.liver.Ins.TC.ratio.RUV.pe
PhosphoExperiment	The PhosphoExperiment class
PhosphoExperiment-class	The PhosphoExperiment class
PhosphoExperiment-method	The PhosphoExperiment class
PhosphoSite.human	PhosphoSitePlus annotations for human
PhosphoSite.mouse	PhosphoSitePlus annotations for mouse
PhosphoSite.rat	PhosphoSitePlus annotations for rat
plotKinaseNetwork	Plot kinase network
plotQC	A set of function for data QC plot
plotSignalomeMap	Plot signalome map
PPE-accessors	PhosphoExperiment object accessors
PPE-operate	PhosphoExperiment object subset, combine methods
ptImpute	Paired-tail (pt) based impute
rbind	PhosphoExperiment object subset, combine methods
rbind-method	PhosphoExperiment object subset, combine methods
Residue	PhosphoExperiment object accessors
Residue-method	PhosphoExperiment object accessors
Residue<-	PhosphoExperiment object accessors
Residue<--method	PhosphoExperiment object accessors
RUVphospho	RUV for phosphoproteomics data normalisation
RUVproteome	RUV for phosphoproteomics data normalisation
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
Sequence	PhosphoExperiment object accessors
Sequence-method	PhosphoExperiment object accessors
Sequence<-	PhosphoExperiment object accessors
Sequence<--method	PhosphoExperiment object accessors
Signalomes	PhosR Signalomes
Site	PhosphoExperiment object accessors
Site-method	PhosphoExperiment object accessors
Site<-	PhosphoExperiment object accessors
Site<--method	PhosphoExperiment object accessors
siteAnnotate	Phosphosite annotation
SPSs	A list of Stably Phosphorylated Sites (SPSs)
standardise	Standardisation
SummarizedExperiment,	The PhosphoExperiment class
tImpute	Tail-based impute
UniprotID	PhosphoExperiment object accessors
UniprotID-method	PhosphoExperiment object accessors
UniprotID<-	PhosphoExperiment object accessors
UniprotID<--method	PhosphoExperiment object accessors
[	PhosphoExperiment object subset, combine methods
[-method	PhosphoExperiment object subset, combine methods
[<-	PhosphoExperiment object subset, combine methods
[<--method	PhosphoExperiment object subset, combine methods