Calculate rarefied diversity metrics through repeated subsampling

Normalize diversity estimates across samples by subsampling to a common depth. This corrects for sequencing depth bias when comparing repertoires.

Usage

iterativeSummary(study_table, iterations, min_count = 1000)

Arguments

study_table

A tibble of antigen receptor sequences from readImmunoSeq(). Must contain "junction_aa", "duplicate_count", and "duplicate_frequency" columns. Use productive junction sequences (not aggregated by amino acid) for accurate clonality estimates.

iterations

Number of bootstrap iterations for rarefaction (default 100). Higher values increase precision but take longer to compute.

min_count

Target sequencing depth for rarefaction (default 1000). Repertoires with fewer sequences than this will be excluded with a warning.

Value

Tibble with diversity metrics averaged across bootstrap iterations