findUniqueIDs: Confirm or List Unique IDs from the netPhorceData

In ksong4/NetPhorce: Phosphoproteomics Network Analysis (NetPhorce)

Confirm or List Unique IDs from the netPhorceData

Description

This function intended to use to confirm the user’s input Unique IDs for plotting or list the avaliable Unique IDs.

Usage

findUniqueIDs(
  netPhorceData = netPhorceData,
  uniqueIDList = NULL,
  verbose = FALSE
)

Arguments

netPhorceData	(Required). Processed netPhorce Object
uniqueIDList	(Required). Vector of unique IDs. If NULL, this function will return all avaliable uniqueIDs.
verbose	(Required). If TRUE, the function will return the available Unique IDs if the user left uniqueIDList as NULL or none of the IDs on the uniqueIDList matched the IDs in the netPhorce data.

Value

list of vectors for matched and unmatched IDs

Examples

## Not run: 
## Loading Two Conditions Example
data("twoConditionsExample")
## Identify the Key Columns
identifiedCols <- confirmColumnNames(rawMaxQuant = twoConditionsExample,
                                    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 = twoConditionsExample,
                                         intensityPattern = "con_time_rep",
                                         verbose = TRUE)
## Process the data based on the identified columns
netPhorceData <- processData(rawMaxQuant = twoConditionsExample,
                             processedColNames = identifiedCols,
                             processedIntensity = intensityCols,
                             minReplication = 3,
                             minLocalProb = 0.75)
## Search for matching IDs
findUniqueIDs(netPhorceData = netPhorceData,
              uniqueIDList = c(
                # Significant Set Examples:
                "AT1G13030.1", "AT1G13360.3", "AT1G42550.1",
                # Unique/Abscence Set Examples
                "AT1G17280.9", "AT1G22310.2", "AT1G23890.2"
              ),
              verbose = TRUE)
## Return all available IDs
findUniqueIDs(netPhorceData = netPhorceData,
              uniqueIDList = NULL)

## End(Not run)

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