Select feature variables of interest — selectFeatureData • MSnbase

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

Laurent Gatto

Examples


library("pRolocdata")
data(hyperLOPIT2015)
## 5 first feature variables
x <- selectFeatureData(hyperLOPIT2015, fcol = 1:5)
fvarLabels(x)
#> [1] "entry.name"          "protein.description" "peptides.rep1"      
#> [4] "peptides.rep2"       "psms.rep1"          
if (FALSE) { # \dontrun{
## select via GUI
x <- selectFeatureData(hyperLOPIT2015)
fvarLabels(x)
} # }