Package 'RforProteomics'

Packages in a biocView

Description

Finds the package names that have a specific biocView.

Usage

getPackagesInBiocView(
  view,
  rep = c("BioCsoft", "BioCann", "BioCexp", "BioCextra"),
  biocVersion
)

Arguments

view	The biocView of interest. For example "Proteomics".
rep	Repository of interest. One of "BioCsoft", "BioCann", "BioCexp" or '"BioCextra"1.
biocVersion	A character with the Bioconductor version of interest. For example "2.14".

Value

An instance of class BiocView. NULL if the the biocView was not found.

Author(s)

Laurent Gatto

---

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)

---

Package descriptions

Description

Format a BiocView as a data.frame.

Usage

packageDF(x, nsub = TRUE, version = TRUE)

Arguments

x	An instance of class BiocView, as produced by getPackagesInBiocView.
nsub	A logical indicating "\n" are to be replaced by a space.
version	A logical specifying if the package version should be added.

Value

A data.frame with package information.

Author(s)

Laurent Gatto

---

Proteomics and MS biocView packages

Description

Searches for all the packages with the "Proteomics" (software), "MassSpectrometry" (software) and "MassSepctrometryData" (data) packages and return their names, titles and versions as a data.frame. The (unexported but documented) underlying functions are RforProteomics:::getPackagesInBiocView (to find relevant package) and RforProteomics:::packageDF (data.frame formatting).

Usage

proteomicsPackages(biocv, cache = FALSE)

massSpectrometryPackages(biocv, cache = FALSE)

massSpectrometryDataPackages(biocv, cache = FALSE)

Arguments

biocv	A character with the Bioconductor version to search for relevant packages. If missing, the running version is used.
cache	A logical indicating whether cached package information should be used. Default is FALSE. All except development versions are up-to-date.

Value

A data.frame with the respective package names, titles and versions.

Author(s)

Laurent Gatto

Examples

head(pp <- proteomicsPackages("3.0"))
ppc <- proteomicsPackages("3.0", cache = TRUE)
all.equal(pp, ppc)

---

Opens the package vignettes

Description

Opens the package and visualisation vignettes.

Usage

RforProteomics()

RProtVis()

RProtViz()

Value

An instance of class vignette. Used for its side effect, opening a vignette.

Author(s)

Laurent Gatto

---