# A Set of Methods and Tools for Comprehensive Analysis of Phosphoproteomics Data

## Documentation for package ‘PhosR’ version 1.18.5

- 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