MALDIquant: referencePeaks-functions – R documentation

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referencePeaks-functions

Creates a reference MassPeaks object.

Description

This function creates a reference MassPeaks object (also called Anchor Peaks) from a list of MassPeaks objects.
Generally it is a combination of binPeaks and filterPeaks

Usage

referencePeaks(l, method=c("strict", "relaxed"), minFrequency=0.9,
               tolerance=0.002)

Arguments

`l`	`list`, list of `MassPeaks` objects.
`method`	bin creation rule (see `binPeaks`).
`minFrequency`	`double`, remove all peaks which occur in less than `minFrequency*length(l)` `MassPeaks` objects.
`tolerance`	`double`, maximal relative deviation of a peak position (mass) to be considered as identical. Must be multiplied by `10^-6` for ppm, e.g. use `tolerance=5e-6` for 5 ppm.

Value

Returns a new MassPeaks objects.
The intensity slot of the returned MassPeaks represents the frequency of this mass position in all samples.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

Examples

## load package
library("MALDIquant")

## create four MassPeaks objects and add them to the list
p<- list(createMassPeaks(mass=1:2, intensity=1:2),
         createMassPeaks(mass=1:3, intensity=1:3),
         createMassPeaks(mass=1:4, intensity=1:4),
         createMassPeaks(mass=1:5, intensity=1:5))

## only use peaks which occur in all MassPeaks objects as reference peaks
refPeaks <- referencePeaks(p, minFrequency=1)

mass(refPeaks)      # 1:2
intensity(refPeaks) # c(1, 1)

MALDIquant

Quantitative Analysis of Mass Spectrometry Data

v1.19.3

GPL (>= 3)

Authors

Sebastian Gibb [aut, cre] (<https://orcid.org/0000-0001-7406-4443>), Korbinian Strimmer [ths] (<https://orcid.org/0000-0001-7917-2056>)

Initial release

2019-05-12