getSignature: Obtain molecular signature

In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

Obtain molecular signature

Description

Extracts a character vector of molecule names making up a molecular signature.

Usage

getGeneSet(object, gene_set, ...)

getMetaboliteSet(object, metabolite_set, ...)

getProteinSet(object, protein_set, ...)

getSignature(object, signature, 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.
...	Used to absorb deprecated arguments or functions.
signature	Character value. The signature of interest.
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().

Details

These functions retrieve molecule names of single signatures.

• getSignature(): A character vector of molecule names from the signature specified.

• getGeneSet(): A character vector of gene names from the gene set specified.

• getMetaboliteSet(): A character vector metabolite names from the metabolite set specified.

• getProteinSet(): A character vector of protein names from the protein set specified.

Value

Character vector.

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