fetchPeptidesInfo {DIAlignR} | R Documentation

## Get scores of all peptides

### Description

Return a scores, pvalues, and qvalues for all peptides from the osw file.

### Usage

    fetchPeptidesInfo(oswName, runType, context)

### Arguments

`oswName` | (char) path to the osw file.
`runType` | (char) This must be one of the strings "DIA_Proteomics", "DIA_IPF", "DIA_Metabolomics".
`context` | (string) Context used in pyprophet peptide. Must be either "run-specific", "experiment-wide", or "global".

### Value

(dataframe) with following columns:

`peptide_id` | (integer) a unique id for each precursor.
`run` | (character) as in SCORE_PEPTIDE.RUN_ID of osw files.
`score` | (numeric) as in SCORE_PEPTIDE.SCORE of osw files.
`pvalue` | (numeric) as in SCORE_PEPTIDE.PVALUE of osw files.
`qvalue` | (numeric) as in SCORE_PEPTIDE.QVALUE of osw files.

### Author(s)

Shubham Gupta, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-07-01

### See Also

`getPeptideQuery, getPeptideScores`

### Examples

    dataPath <- system.file("extdata", package = "DIAlignR")
    fileInfo <- getRunNames(dataPath = dataPath)
    oswName <- fileInfo[["featureFile"]][1]
    ## Not run:
    precursorsInfo <- fetchPeptidesInfo(fileInfo, runType = "DIA_Proteomics", context = "experiment-wide")

    ## End(Not run)

[Package DIAlignR version 2.2.0 Index]