Spectrum: Spectrum class

In lgatto/Spectrum: Spectrum Infrastructure for Mass Spectrometry Data

Description

The Spectrum class is a simple list of elements. There are two classes of elements. Mandatory elements such as the MS level of the spectrum (msLevel), its retention time (rtime), ... that must be of a pre-defined class (see the Spectrum_elements vector for their names and classes). Optional elements with arbitrary names and classes can also be added.

If, as some point, some elements were to become mandatory, their names and classes would simply need to be added to the Spectrum_elements vector.

Object are created with the Spetrum(...) constructor. Spectrum() generates a instance with empty valid values.

Arguments

...	Mandatory spectrum elements or list thereof. See Spectrum_elements for their names and classes.

Examples

## An empty spectrum
sp <- Spectrum()
sp

## Mandatory elements
Spectrum_elements

## Updating mandatory elements
sp$msLevel
class(sp$msLevel)
sp$msLevel <- 2L ## works
sp$msLevel
try(sp$msLevel <- "not an integer")
sp$msLevel

pa <- PeakAnnotation(peaks = list(c(345.3, 345.32, 345.35, 345.39, 345.4),
                                  657.01,
                                  1231.182),
                     annotations = list("a5", "z3", "y7"))
sp$peakAnnotation
sp$peakAnnotation <- pa
sp$peakAnnotation

## Adding arbitrary elements
sp$foo <- "bar"
sp

## All current elements (mandatory and optional) and their
## respective classes
sapply(sp, class)

## Setting intensity and m/z values. These must be set together,
## as these two elements must be of the same length.
mz <- as.numeric(sample(1000, 10))
i <- as.numeric(sample(1e3:1e5, 10))
sp[c("intensity", "mz")] <- list(i, mz)
plot(sp$mz, sp$intensity, type = "h")

lgatto/Spectrum documentation built on May 8, 2019, 9:07 a.m.