accessors {rTANDEM} | R Documentation

## 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]

[Package rTANDEM version 1.27.0 Index]