getRunNames: Get names of all runs

Description Usage Arguments Value Author(s) Examples

View source: R/get_filenames.R

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

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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

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

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