getRunNames: Get names of all runs

In Roestlab/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

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, [e-mail]

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)

Roestlab/DIAlignR documentation built on March 3, 2021, 9:09 a.m.