createListOfSpectra: Create list of Spectra object(s)

In tnaake/MsQualityUtils: What the package does (short line)

Create list of Spectra object(s)

Description

The function createListOfSpectra returns a list of Spectra objects.

When type == "MetIDQ", the function will return a list of length 2. The first entry contains a Spectra object with all features found in the experiment files. The second entry contains a Spectra object with the features found in the experiment files that have available information on their retention time.

When type == "mzML", the function will return a lit of length 1. The entry contains a Spectra object derived from all mzML files in path.

Usage

createListOfSpectra(type = c("MetIDQ", "mzML"), ...)

Arguments

type	character, either "MetIDQ" or "mzML"
...	arguments passed to createListOfSummarizedExperimentFromMetIDQ or createSpectraFromMzML, for instance path

Details

If type == "MetIDQ", the argument rt can be passed to the function. rt has to be a SummarizedExperiment object containing retention time values in the assay slot. By default, createListOfSpectra loads an in-house library of retention time values from the metabolites of the Biocrates MxP Quant 500 kit that are separated by liquid chromatography. The Spectra object only contains the the shared features between se and rt.

Value

list of Spectra object(s)

Author(s)

Thomas Naake

Examples

## type == "MetIDQ"
path <- system.file("metidq", package = "MsQualityUtils")
createListOfSpectra(type = "MetIDQ", path = path, sheet = 1)

## type == "mzML"
path <- system.file("sciex", package = "msdata")
createListOfSpectra(type = "mzML", path = path)

tnaake/MsQualityUtils documentation built on Feb. 3, 2023, 6:32 a.m.