createSpectraFromSummarizedExperiment: Create Spectra object from a SummarizedExperiment object

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

Create Spectra object from a SummarizedExperiment object

Description

Function to create a Spectra object from a SummarizedExperiment object.

Usage

createSpectraFromSummarizedExperiment(se, rt)

Arguments

se	SummarizedExperiment object
rt	SummarizedExperiment object containing the retention time in the assay slot

Details

The sample name (colnames(se)) is taken to create the dataOrigin that is in down-stream functions used to distinguish the origins of the resulting Spectra's entries.

The Spectra object only contains the the shared features between se and rt.

Author(s)

Thomas Naake

Examples

## create rt object
rt <- loadRt()

## create se object
path <- system.file("metidq", package = "MsQualityUtils")
se_l <- createListOfSummarizedExperimentFromMetIDQ(path = path, sheet = 1)
se <- se_l[[1]]

## run createSpectraFromSummarizedExperiment
createSpectraFromSummarizedExperiment(se = se, rt = rt)

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