Obtain molecules of high variability — getVariableMolecules • SPATA2

Extracts results of identifyVariableMolecules().

getVariableMolecules(object, method = NULL, assay_name = activeAssay(object))

Arguments

object: An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.
method: Character value or NULL. If NULL and there are only variable features stored for one method these results are returned, else the method must be specified.
assay_name: Only relevant if the SPATA2 object contains more than one assay: Denotes the assay of interest and thus the molecular modality to use. Defaults to the active assay as set by activateAssay().

Value

Character vector.

Examples


library(SPATA2)
data("example_data")

object <- loadExampleObject("UKF269T")

# default is method = 'vst'
object <- identifyVariableMolecules(object, n_mol = 2000)

# multiple results can be stored simultaneously
object <- identifyVariableMolecules(object, n_mol = 3000, method = "mean.var.plot")

# fails, cause results for two methods are stored and method = NULL
vars_vst <- getVariableMolecules(object)

vars_vst <- getVariableMoleculs(object, method = "vst") # works

# should work
vars_mvp <- getVariableMolecules(object, method = "mean.var.plot")

length(vars_vst)
length(vars_mvp)