Man pages for PYangLab/PhosR
A set of methods and tools for comprehensive analysis of phosphoproteomics data
| createFrequencyMat | Create frequency matrix |
| frequencyScoring | Frequency scoring |
| 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 |
| 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) |
| pathwayOverrepresent | phosphosite/Gene set over-representation analysis |
| pathwayRankBasedEnrichment | Phosphosite/Gene set enrichment analysis |
| phosCollapse | Summarising phosphosites to proteins |
| phospho.cells.Ins | phospho.cells.Ins |
| PhosphoExperiment | The PhosphoExperiment class |
| PhosphoExperiment-methods | PhosphoExperiment object accessors |
| PhosphoExperiment-operate | PhosphoExperiment object subset, combine methods |
| 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 |
| 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 |
| ptImpute | Paired-tail (pt) based impute |
| RUVphospho | 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 |
| Signalomes | PhosR Signalomes |
| siteAnnotate | Phosphosite annotation |
| SPSs | A list of Stably Phosphorylated Sites (SPSs) |
| standardise | Standardisation |
| tImpute | Tail-based impute |
