getRunNames {DIAlignR} | R Documentation

## Get names of all runs

### Description

Fetches all osw files, then, keeps only those runs which has corresponding mzML files. mzML file names must match with RUN.FILENAME columns of osw files.

### Usage

    getRunNames(dataPath, oswMerged = TRUE, params = paramsDIAlignR())

### Arguments

`dataPath` | (char) Path to xics and osw directory.
`oswMerged` | (logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
`params` | (list) parameters are entered as list. Output of the `paramsDIAlignR` function.

### Value

(dataframe) it has five columns:

`spectraFile` | (string) as mentioned in RUN table of osw files.
`runName` | (string) contain respective mzML names without extension.
`spectraFileID` | (string) ID in RUN table of osw files.
`featureFile` | (string) Path to the feature file.
`chromatogramFile` | (string) Path to the chromatogram file.

### Author(s)

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

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-12-14

### Examples

    dataPath <- system.file("extdata", package = "DIAlignR")
    getRunNames(dataPath = dataPath, oswMerged = TRUE)

[Package DIAlignR version 2.2.0 Index]