selectFeatureData: Select feature variables of interest

In lgatto/MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Select feature variables of interest

Description

Select feature variables to be retained.

requiredFvarLabels returns a character vector with the required feature data variable names (fvarLabels, i.e. the column names in the fData data.frame) for the specified object.

Usage

selectFeatureData(object, graphics = TRUE, fcol)

requiredFvarLabels(x = c("OnDiskMSnExp", "MSnExp", "MSnSet"))

Arguments

object	An MSnSet, MSnExp or OnDiskMSnExp.
graphics	A logical (default is TRUE) indicating whether a shiny application should be used if available. Otherwise, a text menu is used. Ignored if k is not missing.
fcol	A numeric, logical or character of valid feature variables to be passed directly.
x	character(1) specifying the class name for which the required feature data variable names should be returned.

Value

For selectFeatureData: updated object containing only selected feature variables.

For requiredFvarLabels: character with the required feature variable names.

Author(s)

Laurent Gatto

Examples

library("pRolocdata")
data(hyperLOPIT2015)
## 5 first feature variables
x <- selectFeatureData(hyperLOPIT2015, fcol = 1:5)
fvarLabels(x)
## Not run: 
## select via GUI
x <- selectFeatureData(hyperLOPIT2015)
fvarLabels(x)

## End(Not run)

## Subset the feature data of an OnDiskMSnExp object to the minimal
## required columns
f <- system.file("microtofq/MM14.mzML", package = "msdata")
od <- readMSData(f, mode = "onDisk")

## what columns do we have?
fvarLabels(od)

## Reduce the feature data data.frame to the required columns only
od <- selectFeatureData(od, fcol = requiredFvarLabels(class(od)))
fvarLabels(od)

lgatto/MSnbase documentation built on Nov. 12, 2024, 10:58 a.m.