peptideConnectivityTest {ProCoNA} | R Documentation |
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.
peptideConnectivityTest(pnet, pepInfo, pepCol, protCol, repsPerProt)
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 |
Returns a list of the connected peptides and the random samples.
David L Gibbs
data(ProCoNA_Data) #net1 <- buildProconaNetwork("peptide network", peptideData, pow=12) p <- peptideConnectivityTest(net1, masstagdb, "Mass_Tag_ID", "Reference", 200)