For a given vector of protein group names, outputs the names of those protein groups for which none of its member proteins is present in a smaller protein group.
A vector of characters or factors containing single proteins and/or protein groups (i.e. proteins separated by a separator symbol).
The character string that is used to separate the indivudual protein names in each protein group.
A character vector containing the names of the protein groups for which none of its proteins is present in a smaller protein group.
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#This example will give the names of the protein groups in the MSnSet object peptidesCPTAC for which none of its proteins is present in a smaller protein group. library("MSnbase") #Select the columns containing intensities colInt <- grepEcols(system.file("extdata/CPTAC", "peptides.txt", package = "MSqRob"), pattern="Intensity.", split = "\t") #Import MaxQuant's peptides.txt file and convert it to an MSnSet object peptidesCPTAC <- readMSnSet2(system.file("extdata/CPTAC", "peptides.txt", package = "MSqRob"), ecol = colInt, sep = "\t") #Our approach: a peptide can map to multiple proteins, as long as there is none of these proteins present in a smaller subgroup. groups <- smallestUniqueGroups(fData(peptidesCPTAC)$Proteins) groups
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