renameADT-methods: Replace ADT names in an object containing ADT expression

In HelenLindsay/AbNames: Standardize Antibody Names

Replace ADT names in an object containing ADT expression

Description

Given an object containing antibody derived tag (ADT) expression measurements, such as a [SingleCellExperiment::SingleCellExperiment()] or [MultiAssayExperiment::MultiAssayExperiment()] and a vector of new names, replace the names of the ADTs and store the original names as metadata.

Used for e.g. standardising protein names across studies. See 'getCommonName()' for generating standardised names by matching to the citeseq data set. Names have to be provided because we recommend manually checking standard names.

Usage

renameADT(obj, names, ...)

## S4 method for signature 'SingleCellExperiment,character'
renameADT(obj, names, assay = "ADT", ...)

## S4 method for signature 'MultiAssayExperiment,character'
renameADT(obj, names, assay = "counts", ...)

Arguments

obj	An object containing ADT expression measurements
names	A character vector of new names, equal to the number of ADTs in obj
...	Not currently used
assay	Name of the assay to be renamed (Default: "counts")

Value

An object of the same class as obj, with ADT measurements renamed

Author(s)

Helen Lindsay

HelenLindsay/AbNames documentation built on June 6, 2023, 1:18 p.m.