getVariableMolecules: Obtain molecules of high variability

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Obtain molecules of high variability

Description

Extracts results of identifyVariableMolecules().

Usage

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)

theMILOlab/SPATA2 documentation built on Feb. 8, 2025, 11:41 p.m.