selectFeatureData {MSnbase} | R Documentation

## 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)

[Package MSnbase version 2.12.0 Index]