Function reference • NetPhorce

Demonstration Data
`oneConditionExample`	A MaxQuant result file of an experiment with one experimental condition and 5 time points.
`twoConditionsExample`	A MaxQuant result file of an experiment with two experimental conditions and 5 time points.
`kinasesPhosphatases`	Pre-loaded Kinase/Phosphatase Table for 25 Species
Pre-processing Raw Data
`confirmColumnNames()`	Identify the Columns needed for Data Processing
`confirmIntensityColumns()`	Identify the Intensity Columns
Validate Raw Data
`processData()`	Initial processing and quality control of MaxQuant data including the removal of contaminated and reverse peptides, unnecessary columns, and invalid peptides based on filtering criteria.
Pre-Processing for Network Analysis
`checkPreloadKinaseTable()`	Print a summary kinase/phosphatase table
`validateKinaseTable()`	Validate existing or user-uploaded Kinase/Phosphatase data
`regulationCheck()`	The regulation check based on the input parameter for the Network Analysis
Network Analysis
`networkAnalysis()`	Network Analysis
Extract/Convert Processed Data
`extractSummaryTable()`	Extract a summary table from processed NetPhorce data
`extractNetworkResults()`	Extract the network inference results from processed NetPhorce data
`convertShinyToR()`	Load Shiny Plot Object to R
Preprocessing Data for Plotting
`findClusters()`	Identify and Validate Provided Clusters for plotUniqueIDsHeatmaps
`findPeptideIDs()`	Identify provided peptide IDs for plotting
`findUniqueIDs()`	Confirm or List Unique IDs from the netPhorceData
Plotting
`plotDistribution()`	Plot the Distribution of the Intensity Data
`plotHistBox()`	Plot the Distribution of the Intensity Data
`plotPCA()`	PCA Plot
`plotClustersHeatmap()`	Plot Heatmap Based on the Clusters Verified from the `findClusters` function
`plotUniqueIDsHeatmaps()`	Plot Heatmap Based on the Unique IDs Verified from the `findUniqueIDs` function
`plotSinglePeptide()`	Dotplot displaying the log2 intensity of a single phosphopeptide across the different time points and for each condition.
`plotMultiPeptides()`	Intensity pattern of a single or multiple phosphopeptide across the time course and for each condition.
`plotNetPhorce()`	A VisNetwork plot of the inferred network
`plotRegulation()`	The regulation plot allows for the users to visually evaluate the chosen thresholds.

Reference

Demonstration Data

Pre-processing Raw Data

Validate Raw Data

Pre-Processing for Network Analysis

Network Analysis

Extract/Convert Processed Data

Preprocessing Data for Plotting

Plotting