TCRrep S4 class

Represents a T-cell receptor repertoire with associated metadata, distance matrices, and analysis results. This is the central data object of the tcrdistR package. Create instances using the TCRrep constructor rather than calling new("TCRrep", ...) directly.

Slots

clone_df: A data.frame of clonotypes. Required columns depend on the chains value: alpha-beta ("AB") requires va, cdr3a, vb, cdr3b; alpha only ("A") requires va, cdr3a; beta only ("B") requires vb, cdr3b; gamma-delta ("GD") requires va, cdr3a, vb, cdr3b.
organism: Character string specifying the organism. Must be one of the organisms available in the bundled gene database (e.g. "human", "mouse").
chains: Character string specifying the chain combination. One of "AB", "A", "B", or "GD".
metric: Character string specifying the distance metric. One of "tcrdist" or "hamming".
weights: A named list with elements cdr3 and v_region specifying the integer weights applied to each region's distance contribution.
gap_penalties: A named list with elements cdr3 and v_region specifying the integer gap penalties used in sequence alignment.
dist_a: Distance matrix for alpha-chain only comparisons. Either NULL or a numeric matrix.
dist_b: Distance matrix for beta-chain only comparisons. Either NULL or a numeric matrix.
paired_dist: Paired (alpha + beta combined) distance matrix. Either NULL or a numeric matrix. Populated when compute_distances = TRUE is passed to TCRrep.
knn_indices: K-nearest-neighbour index matrix. Either NULL or an integer matrix of dimensions N x K.
knn_distances: K-nearest-neighbour distance matrix. Either NULL or a numeric matrix of dimensions N x K.
rep_dists: A named list of representative-clonotype distance objects, populated by downstream analyses.
meta_clonotypes: Meta-clonotype table. Either NULL or a data.frame.
motifs: A named list of motif objects, populated by downstream analyses.

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See also