getRefRun {DIAlignR} | R Documentation

## Fetch the reference run for each peptide

### Description

Provides the reference run based on lowest p-value.

### Usage

    getRefRun(peptideScores, applyFun = lapply)

### Arguments

`peptideScores` | (list of data-frames) each dataframe has scores of a peptide across all runs.
`applyFun` | (function) value must be either lapply or BiocParallel::bplapply.

### Value

(dataframe) has two columns:

`peptide_id` | (integer) a unique id for each peptide.
`run` | (string) run identifier.

### Author(s)

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

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-04-08

### See Also

`getPeptideScores`

### 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)
    peptideIDs <- unique(precursorsInfo$peptide_id)
    peptidesInfo <- getPeptideScores(fileInfo, peptideIDs)
    peptidesInfo <- lapply(peptideIDs, function(pep) peptidesInfo [.(pep),])
    names(peptidesInfo) <- as.character(peptideIDs)
    getRefRun(peptidesInfo)

[Package DIAlignR version 2.2.0 Index]