Return the input ID when avaiable in the dataset or output all available IDs
findPeptideIDs(netPhorceData = netPhorceData, peptideIDList = NULL)Processed NetPhorce Object
A single or multiple peptide IDs. The peptide ID consists of a combination of the protein ID, amino acid, and multiplicity. If left as NULL, the full table of available IDs will be printed.
list of data.frames
if (FALSE) {
## 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)
## Extract peptides from the NetPhorce Data
findPeptideIDs(netPhorceData = netPhorceData,
peptideIDList = c("AT1G01320.2_S1349_1",
"AT1G05560.1_S153_1",
"AT1G01320.2_S149_1"))
}