accessors {rTANDEM} | R Documentation |
The GetProteins
, GetPeptides
and GetDegeneracy
functions are used to extract information from the rTANDEM result object.
GetProteins(results, log.expect=0, min.peptides=1L) GetPeptides(protein.uid, results, expect=1, score=0) GetDegeneracy(peptide.id, results)
results |
An object of the class rTResult that contains the result of an rTANDEM or X!Tandem analysis. |
log.expect |
X!Tandem provides a score of protein identification that is presented in terms of the log of the expect value of the identification. This score can be used as a threshold to discard low confidence identifications from the protein list. |
expect |
The expect value of peptide identification. This statistic can be used as a threshold to discard low confidence identifications from the peptide list. |
min.peptides |
The number of peptides involved in the identification of a given protein is computed. This number can be used as a threshold to discard identifications based on too few peptides from the protein list. |
protein.uid |
The tandem identifier of the protein (a numeric). |
peptide.id |
The tandem identifier of the peptide (a character). |
score |
The tandem score of the peptide identification. This score can be used as a threshold to discard low confidence identifications from the peptide list. |
GetProteins
and GetDegeneracy
return a data.table
of proteins. GetPeptides
returns a data.table of peptides with
their ptm (post-translational modifications). Note that this table is
generated through a merge of the peptide table and the ptm table:
hence, if peptides has two ptm, it will occupy to rows in
the resulting data.table.
# To show how to use the accessor functions, we need an rTANDEM result. # We can produce one by running the example from the rTANDEM function, # and reading it to R with GetResultsFromXML: # output.file.path <- example(rTANDEM) results <- GetResultsFromXML(output.file.path[[1]]) # To get a data.table of the proteins identified by at least 2 peptides # and with an expect value of 0.05 or better: proteins <- GetProteins(results, log.expect=-1.3, min.peptides=2) proteins[, -c(4,5), with=FALSE] # Colums are removed for better display # To get a list of the peptides used to identify the first protein # (YCR012W, uid=576): peptides <- GetPeptides(protein.uid="576", results) peptides # To get the list of proteins to which proteins a peptide belongs: # (If a peptide belongs to more than one protein, it should not be # used for quantification, as a biomarker or a MRM target.) proteins.of.the.peptide <- GetDegeneracy(peptide.id="169.1.1", results) proteins.of.the.peptide[,label]