MSnbase: fData-utils – R documentation

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fData-utils

Expand or merge feature variables

Description

The expandFeatureVars and mergeFeatureVars respectively expand and merge groups of feature variables. Using these functions, a set of columns in a feature data can be merged into a single new data.frame-column variables and a data.frame-column can be expanded into single feature columns. The original feature variables are removed.

Usage

expandFeatureVars(x, fcol, prefix)

mergeFeatureVars(x, fcol, fcol2)

Arguments

`x`	An object of class `MSnSet`.
`fcol`	A `character()` of feature variables to expand (for `expandFeatureVars`) or merge (for `mergeFeatureVars`).
`prefix`	A `character(1)` to use as prefix to the new feature variables. If missing (default), then `fcol` is used instead. If `NULL`, then no prefix is used.
`fcol2`	A `character(1)` defining the name of the new feature variable.

Value

An MSnSet for expanded (merged) feature variables.

Author(s)

Laurent Gatto

Examples

library("pRolocdata")
data(hyperLOPIT2015)
fvarLabels(hyperLOPIT2015)
## Let's merge all svm prediction feature variables
(k <- grep("^svm", fvarLabels(hyperLOPIT2015), value = TRUE))
hl <- mergeFeatureVars(hyperLOPIT2015, fcol = k, fcol2 = "SVM")
fvarLabels(hl)
head(fData(hl)$SVM)

## Let's expand the new SVM into individual columns
hl2 <- expandFeatureVars(hl, "SVM")
fvarLabels(hl2)
## We can set the prefix manually
hl2 <- expandFeatureVars(hl, "SVM", prefix = "Expanded")
fvarLabels(hl2)
## If we don't want any prefix
hl2 <- expandFeatureVars(hl, "SVM", prefix = NULL)
fvarLabels(hl2)

MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics

v2.16.1

Artistic-2.0

Authors

Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker and Lieven Clement.

Initial release