Obtain molecular signature — getGeneSet • SPATA2

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

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().

Value

Character vector.

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.