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

## Documentation for package ‘PhosR’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

createFrequencyMat | Create frequency matrix
frequencyScoring | Frequency scoring
KinaseFamily | KinaseFamily
kinaseSubstrateHeatmap | Kinase-substrate annotation prioritisation heatmap
kinaseSubstratePred | kinaseSubstratePred
kinaseSubstrateProfile | Kinase substrate profiling
kinaseSubstrateScore | Kinase substrate scoring
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
mUnion | Multi-intersection, union
pathwayOverrepresent | Gene set over-representation analysis
pathwayRankBasedEnrichment | Gene set enrichment analysis
Pathways.KEGG | KEGG pathway annotations
Pathways.reactome | Reactome pathway annotations
phosCollapse | Summarising phosphosites to proteins
phospho.cells.Ins | phospho.cells.Ins
phospho.L6.ratio | phospho.L6.ratio
phospho.liver.Ins.TC.ratio.RUV | phospho_liverInsTC_RUV_sample
PhosphoSite.human | PhosphoSitePlus annotations for human
PhosphoSite.mouse | PhosphoSitePlus annotations for mouse
PhosphoSite.rat | PhosphoSitePlus annotations for rat
plotQC | A set of function for data QC plot
ptImpute | Paired-tail (pt) based impute
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)
selectOverallPercent | Select phosphosite by percentage of quantification
selectTimes | selectTimes
Signalomes | PhosR Signalomes
siteAnnotate | Phosphosite annotation
SPSs | A list of Stably Phosphorylated Sites (SPSs)
standardise | Standardisation
tImpute | Tail-based impute