id_quality {MSnID} | R Documentation

## Identification quality

### Description

Reports quality for a given level of identification (spectra, peptide or protein).

### Usage

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

### Arguments

`object` | An instance of class "MSnID".
`filter` | Optional argument. 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` `evaluate_filter`

### Examples

    data(c_elegans)
    id_quality(msnidObj, level="peptide")
    id_quality(msnidObj, filter="`MS-GF:PepQValue` < 0.01", level="peptide")

[Package MSnID version 1.24.0 Index]