extractNetworkResults: Extract the network inference results from processed...

In ksong4/NetPhorce: Phosphoproteomics Network Analysis (NetPhorce)

Extract the network inference results from processed NetPhorce data

Description

Obtain the network inference from NetPhorce data after networkAnalysis.

Usage

extractNetworkResults(netPhorceData = netPhorceData)

Arguments

netPhorceData

Processed NetPhorce Object

Value

A single data.frame

Examples

## Not run: 
## Loading One Condition Data
data("oneConditionExample")
## Identify the Key Columns
identifiedCols <- confirmColumnNames(rawMaxQuant = oneConditionExample,
                                    positionCol = "Position",
                                    reverseCol = "Reverse",
                                    localizationProbCol = "Localization prob",
                                    potentialContaminationCol = "Potential contaminant",
                                    aminoAcidCol = "Amino acid",
                                    uniqueIDCol = "Protein",
                                    seqWindowIDCol = "Sequence window",
                                    fastaIDCol = "Fasta headers")
## Identify the Intensity Columns with Condition, Time Point and Replication Information
intensityCols <- confirmIntensityColumns(rawMaxQuant = oneConditionExample,
                                         intensityPattern = "con_time_rep",
                                         verbose = TRUE)
## Process the data based on the identified columns
netPhorceData <- processData(rawMaxQuant = oneConditionExample,
                             processedColNames = identifiedCols,
                             processedIntensity = intensityCols,
                             minReplication = 3,
                             minLocalProb = 0.75)

## Confirm the correct Kinase/Phosphotase information for the data
netPhorceData <- validateKinaseTable(netPhorceData = netPhorceData,
                                     defaultKinaseTable = TRUE,
                                     abbrev = "Ath")
## Evaluate the netPhorce object with regulation thresholds
netPhorceData <- regulationCheck(netPhorceData = netPhorceData,
                                 upReg = 0.25,
                                 downReg = 0.25,
                                 absMinThreshold = 0.1,
                                 qValueCutOff = 0.05,
                                 verbose = TRUE)
## Network Analysis
netPhorceData <- networkAnalysis(netPhorceData = netPhorceData,
                               requestPlotData = TRUE)
## Extract Network Results
networkResults <- extractNetworkResults(netPhorceData = netPhorceData)

## End(Not run)

ksong4/NetPhorce documentation built on March 24, 2023, 12:51 p.m.