getPeptideScores {DIAlignR} | R Documentation

## Get scores of peptide

### Description

Get a list of dataframes that contains peptide scores, pvalues, and qvalues across all runs.

### Usage

    getPeptideScores(
      fileInfo,
      peptides,
      oswMerged = TRUE,
      runType = "DIA_Proteomics",
      context = "global"
    )

### Arguments

`fileInfo` | (data-frame) Output of `getRunNames` function.
`peptides` | (integer) Ids of peptides for which scores are required.
`oswMerged` | (logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
`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

(list of dataframes) dataframe has 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

`getRunNames, fetchPeptidesInfo`

### Examples

    dataPath <- system.file("extdata", package = "DIAlignR")
    fileInfo <- getRunNames(dataPath = dataPath)
    precursorsInfo <- getPrecursors(fileInfo, oswMerged = TRUE, runType = "DIA_Proteomics",
    context = "experiment-wide", maxPeptideFdr = 0.05)
    peptidesInfo <- getPeptideScores(fileInfo, unique(precursorsInfo$peptide_id))
    dim(peptidesInfo) # 684 5

[Package DIAlignR version 2.2.0 Index]