ProCoNA (version 1.8.0)

peptideConnectivityTest: peptideConnectivityTest

Description

This function will compare the connectivity between peptides mapped to a given protein, against a randomly drawn, similarly sized, selection of peptides. The hypothesis is that peptides from a given protein should be more connected than random.

Usage

peptideConnectivityTest(pnet, pepInfo, pepCol, protCol, repsPerProt)

Arguments

pnet

The peptide net object

pepInfo

The peptide information table, mapping peptides to proteins

pepCol

The string identifying the column in the pepInfo table with peptide ID

protCol

String identifying column in pepInfo with Protein ID.

repsPerProt

number of repetitions for the null

Value

Examples

data(ProCoNA_Data)
#net1 <- buildProconaNetwork("peptide network", peptideData, pow=12)
p <- peptideConnectivityTest(net1, masstagdb, "Mass_Tag_ID", "Reference", 200)