downsample_immundata: Downsample ImmunData annotations at the repertoire level

In immundata: A Unified Data Layer for Large-Scale Single-Cell, Spatial and Bulk Immunomics

Downsample ImmunData annotations at the repertoire level

Description

Downsamples an ImmunData object by selecting barcodes within each repertoire. If repertoire schema is not defined, the entire dataset is treated as one repertoire.

The function uses a single parameter n:

• If ⁠0 < n < 1⁠, n is treated as a proportion of repertoire size.

• If n > 1, n is treated as an absolute target count.

• If n == 1, an error is raised.

Downsampling is barcode-based. For count-based inputs (e.g. bulk), per-barcode counts (imd_n_chains) are trimmed when needed to reach the target.

Usage

downsample_immundata(idata, n, seed = NULL)

Arguments

idata	An ImmunData object.
n	Numeric scalar controlling downsampling amount. See details for interpretation.
seed	Optional integer scalar for reproducible sampling.

Value

A new ImmunData object with downsampled annotations.

immundata documentation built on April 4, 2026, 9:09 a.m.