extractPseudospectra: Extract pseudospectra

In tdepke/CluMSID: Clustering of MS2 Spectra for Metabolite Identification

Extract pseudospectra

Description

extractPseudospectra() is used to extract MS1 pseudospectra from CAMERA output.

Usage

extractPseudospectra(x, min_peaks = 1, intensity_columns = NULL)

Arguments

x	CAMERA output that contains information on pseudospectra. Can either be of class data.frame or xsAnnotate. It is recommended to use either xsAnnotate objects or data.frames generated from XCMSonline results tables but other data.frames are possible.
min_peaks	Minimum number of peaks in pseudospectrum, defaults to 1. See extractMS2spectra.
intensity_columns	Numeric, defaults to NULL. If a data.frame is used as input which has not been generated from an XCMSonline results table, the indices of the columns that contain the peak intensities in the different samples have to be indicated as intensity_columns.

Value

A list of pseudospectra, stored as objects of class pseudospectrum, analogous to the output of extractMS2spectra.

Examples

pstable <- readr::read_delim(file = system.file("extdata",
                                "TD035_XCMS.annotated.diffreport.tsv",
                                package = "CluMSIDdata"), delim = "\t")

pseudospeclist <- extractPseudospectra(pstable, min_peaks = 2)

tdepke/CluMSID documentation built on April 10, 2022, noon