evaluate_filter {MSnID} | R Documentation

## Filters the MS/MS identifications

### Description

Filter out peptide-to-spectrum MS/MS identifications.

### Usage

        evaluate_filter(object, filter, level=c("PSM", "peptide", "accession"))

### Arguments

`object` | An instance of class "MSnID".
`filter` | Either an instance of MSnIDFilter class or a `"character"`.
`level` | Level at which the filter will be evaluated. Possible values are "PSM", "peptide" and "accession". Multiple are OK. Default is all of them.

### Value

Returns a matrix with with column names "fdr" and "n". Column "n" contains the number of features (spectra, peptides or proteins/accessions) passing the filter. Column "fdr" is the false discovery rate (i.e. identification confidence) for the corresponding features. Row names correspond to the provided levels.

### Author(s)

Vladislav A Petyuk vladislav.petyuk@pnnl.gov

### See Also

`MSnID` `id_quality`

### Examples

    data(c_elegans)

    ## Filtering using string:
    msnidObj <- assess_termini(msnidObj, validCleavagePattern="[KR]\\.[^P]")
    table(msnidObj$numIrregCleavages)
    evaluate_filter(msnidObj, "numIrregCleavages == 0")

    ## Filtering using filter object:
    # first adding columns that will be used as filters
    msnidObj$msmsScore <- -log10(msnidObj$`MS-GF:SpecEValue`)
    msnidObj$mzError <- abs(msnidObj$experimentalMassToCharge -
                            msnidObj$calculatedMassToCharge)
    # setting up filter object
    filtObj <- MSnIDFilter(msnidObj)
    filtObj$msmsScore <- list(comparison=">", threshold=10.0)
    filtObj$mzError <- list(comparison="<", threshold=0.1) # 0.1 Thomson
    show(filtObj)
    evaluate_filter(msnidObj, filtObj)

[Package MSnID version 1.16.1 Index]