Package index • SmartPhos

All functions

Homo_sapien_kinase_substrate_network: Homo_sapien_kinase_substrate_network

Mus_musculus_kinase_substrate_network: Mus_musculus_kinase_substrate_network

addZeroTime(): Add Zero Timepoint Data to Treatment Subset

calcKinaseScore(): Calculate Kinase Activity Scores using decoupleR

checkRatioMat(): Check the PP/FP ratio matrix and remove feature that do not meet requirements

clusterEnrich(): Perform Cluster Enrichment Analysis

clusterTS(): Perform Clustering on Time-Series Data

dda_example: dda_example

dia_example: dia_example

enrichDifferential(): Perform Enrichment analysis on differentially expressed genes or phospho-sites

generateInputTable(): Generate Input Table for Proteomic and Phosphoproteomic Analysis

generateInputTable_DIA(): Generate Input Table for DIA Analysis

getDecouplerNetwork(): Load Kinase-Substrate Interaction Network

getOneSymbol(): Extract the Last Gene Symbol from a Semicolon-Separated List

getRatioMatrix(): Get Ratio Matrix of Phosphoproteome Data

intensityBoxPlot(): Plot Boxplot of Intensity Data

makeSmartPhosDirectory(): Create SmartPhos Directory Structure

medianNorm(): Normalize a Matrix Using Median or Mean

mscale(): Scale and Center a Matrix

normByFullProteome(): Normalize Phosphoproteome by Full Proteome

performCombinedNormalization(): Perform Combined Normalization on MultiAssayExperiment Data

performDifferentialExp(): Perform Differential Expression Analysis

plotAdjustmentResults(): Plot Adjustment Results

plotHeatmap(): Plot Heatmap of Intensity assay

plotIntensity(): Plot Intensity Boxplots

plotKinaseDE(): Plot Kinase score for Differential Expression data

plotKinaseTimeSeries(): Plot Kinase Activity Time Series

plotLogRatio(): Plot Log Ratio of PP/FP (Phosphoproteome to Full Proteome) intensities

plotMissing(): Plot Missing Data Completeness

plotPCA(): Plot PCA

plotTimeSeries(): Plot Time Series Data for a gene or phospho site from SummarizedExperiment object

plotVolcano(): Plot Volcano Plot for Differential Expression Analysis

preprocessPhos(): Preprocess Phosphoproteome Data

preprocessProteome(): Preprocess Proteome Data

readExperiment(): Read and Process the DDA experiment.

readExperimentDIA(): Read and Process a DIA Experiment

readOnePhos(): Read and Filter Phosphorylation Data for a Specific Sample

readOnePhosDIA(): Read Phosphorylation Data for One Sample from DIA

readOneProteom(): Read and Process One Proteomics Sample

readOneProteomDIA(): Read and Process a Single DIA Proteomics Sample

readPhosphoExperiment(): Read Phosphorylation Experiment Data

readPhosphoExperimentDIA(): Read Phosphorylation Experiment Data from DIA

readProteomeExperiment(): Read and Process Proteomics Experiment Data

readProteomeExperimentDIA(): Read and Process a DIA Proteome Experiment

runFisher(): Perform Fisher's Exact Test on Gene Sets

runGSEAforPhospho(): Run GSEA for Phosphorylation Data

runPhosphoAdjustment(): Run Phospho Adjustment

runSmartPhos(): Launch the SmartPhos Shiny Application

splineFilter(): Filter Expression Matrix Using Spline Models

swissProt: swissProt