rTANDEM (version 1.12.0)

accessors: Extract information from rTANDEM result object

Description

The GetProteins, GetPeptides and GetDegeneracy functions are used to extract information from the rTANDEM result object.

Usage

GetProteins(results, log.expect=0, min.peptides=1L)
GetPeptides(protein.uid, results, expect=1, score=0)
GetDegeneracy(peptide.id, results)

Arguments

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.

Value

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.

Examples

# 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]