mstut: Create, analyse and detect ions

In lgatto/RforProteomics: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication

Create, analyse and detect ions

Description

This is the constructor function to generate a set of ions that can later be analysed with 'analyse()' and detected with 'detect()'.

Usage

new_ions(npeaks = 10, mzrange = c(100, 1000), nimg = 100)

analyse(x, sleep = 0.1)

analyze(x, sleep = 0.1)

detect(x, new = FALSE)

spectrum(x, ...)

Arguments

npeaks	A 'numeric' scalar defining the number of unique peaks (M/Z values). Default is 10.
mzrange	A 'numeric' of length 2 defining the range of possible M/Z values. Default is 'c(100, 1000)'.
nimg	A 'numeric' scalar. When analysing the ions, their separation along their M/Z values will be split along a sequence of length 'nimg'. Default is 100.
x	An object of class 'ions'.
sleep	How much time to wait before producing the next plot.
new	A 'logical' scalar, indicating if the separated ions (last frame of calling 'analyse) should be plotting, or whether the detection should be overlaid. Default is 'FALSE', to add the plot on top of the opened device.
...	Additional arguments passed to [graphics::plot()].

Value

An object of class 'ions'.

'analyse', 'detect' and 'spectrum' are used for their side effect or producing plots. They all invisibly return 'NULL'.

Author(s)

Laurent Gatto

Examples

set.seed(1L)
x <- new_ions(nimg = 5)
x
analyse(x)
detect(x)
spectrum(x)

lgatto/RforProteomics documentation built on May 10, 2023, 11:51 p.m.