selectFeatureData: Select feature variables of interest
In MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Description Usage Arguments Value Author(s) Examples

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.

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selectFeatureData(object, graphics = TRUE, fcol)

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

`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.

For selectFeatureData: updated object containing only selected feature variables.

For requiredFvarLabels: character with the required feature variable names.

Laurent Gatto

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)