getSpectrum: Access individual spectra from a list of spectra by various...

Description Usage Arguments Value Examples

View source: R/accessory_functions.R

Description

As accessing S4 objects within lists is not trivial, getSpectrum can be used to access individual or several MS2spectrum objects by their slot entries.

Usage

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getSpectrum(featlist, slot, what, mz.tol = 1e-05, rt.tol = 30)

Arguments

featlist

a list that contains only objects of class MS2spectrum

slot

The slot to be searched (invalid slot arguments will produce errors). Possible values are:

  • 'id'

  • 'annotation'

  • 'precursor' (m/z of precursor ion)

  • 'rt' (retention time of precursor)

what

the search term or number, must be character for 'id' and 'annotation' and numeric for 'precursor' and 'rt' See vignette for examples.

mz.tol

the tolerance used for precursor ion *m/z* searches, defaults to 1E-05 (+/- 10ppm)

rt.tol

the tolerance used for precursor ion retention time searches, defaults to 30s; high values can be used to specify retention time ranges (see vignette for example)

Value

If the only one spectrum matches the search criteria, the output is an object of class MS2spectrum; if more than one spectrum matches, the output is a list of MS2spectrum objects.

Examples

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load(file = system.file("extdata",
    "annotatedSpeclist.RData",
    package = "CluMSIDdata"))

getSpectrum(annotatedSpeclist, "annotation", "pyocyanin")

getSpectrum(annotatedSpeclist, "id", "M244.17T796.4")

getSpectrum(annotatedSpeclist, "precursor", 286.18, mz.tol = 1E-03)

six_eight <- getSpectrum(annotatedSpeclist, "rt", 420, rt.tol = 60)

CluMSID documentation built on April 29, 2020, 5:20 a.m.