joinPeaks: Join (map) peaks of two spectra

In Spectra: Spectra Infrastructure for Mass Spectrometry Data

Description

These functions map peaks from two spectra with each other if the difference between their m/z values is smaller than defined with parameters tolerance and ppm. All functions take two matrices

• joinPeaks: maps peaks from two spectra allowing to specify the type of join that should be performed: type = "outer" each peak in x will be matched with each peak in y, for peaks that do not match any peak in the other spectra an NA intensity is returned. With type = "left" all peaks from the left spectrum (x) will be matched with peaks in y. Peaks in y that do not match any peak in x are omitted. type = "right" is the same as type = "left" only for y. Only peaks that can be matched between x and y are returned by type = "inner", i.e. only peaks present in both spectra are reported.

Usage

joinPeaks(x, y, type = "outer", tolerance = 0, ppm = 10, ...)

Arguments

x	matrix with two columns "mz" and "intensity" containing the m/z and intensity values of the mass peaks of a spectrum.
y	matrix with two columns "mz" and "intensity" containing the m/z and intensity values of the mass peaks of a spectrum.
type	For joinPeaks: character(1) specifying the type of join that should be performed. See function description for details.
tolerance	numeric(1) defining a constant maximal accepted difference between m/z values of peaks from the two spectra to be matched/mapped.
ppm	numeric(1) defining a relative, m/z-dependent, maximal accepted difference between m/z values of peaks from the two spectra to be matched/mapped.
...	option parameters.

Value

All functions return a list of elements "x" and "y" each being a two column matrix with m/z (first column) and intensity values (second column). The two matrices contain the matched peaks between input matrices x and y and hence have the same number of rows. Peaks present in x but not in the y input matrix have m/z and intensity values of NA in the result matrix for y (and vice versa).

Implementation notes

A mapping function must take two numeric matrices x and y as input and must return list with two elements named "x" and "y" that represent the aligned input matrices. The function should also have ... in its definition. Parameters ppm and tolerance are suggested but not required.

Author(s)

Johannes Rainer

Examples

x <- cbind(c(31.34, 50.14, 60.3, 120.9, 230, 514.13, 874.1),
    1:7)
y <- cbind(c(12, 31.35, 70.3, 120.9 + ppm(120.9, 5),
    230 + ppm(230, 10), 315, 514.14, 901, 1202),
    1:9)

## No peaks with identical m/z
joinPeaks(x, y, ppm = 0, type = "inner")

## With ppm 10 two peaks are overlapping
joinPeaks(x, y, ppm = 10, type = "inner")

## Outer join: contain all peaks from x and y
joinPeaks(x, y, ppm = 10, type = "outer")

## Left join: keep all peaks from x and those from y that match
joinPeaks(x, y, ppm = 10, type = "left")

## Right join: keep all peaks from y and those from x that match. Using
## a constant tolerance of 0.01
joinPeaks(x, y, tolerance = 0.01, type = "right")

Spectra documentation built on Nov. 27, 2020, 2 a.m.