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K-nearest-neighbors from a precomputed distance matrix

Source: R/wrappers_neighbors.R
knn_from_matrix.Rd

Extracts K nearest neighbors for each row of a precomputed N x N distance matrix D, with optional same-group masking.

Usage

knn_from_matrix(D, K, agroups = NULL, bgroups = NULL, sort_nbrs = TRUE)

Arguments

D

Numeric matrix (N x N). Precomputed pairwise distance matrix. Must be square.

K

Integer. Number of nearest neighbors to return. Must satisfy 1 <= K <= N - 1.

agroups

Integer vector of length N, or NULL. Alpha-chain group assignments. NULL assigns unique groups (no masking).

bgroups

Integer vector of length N, or NULL. Beta-chain group assignments.

sort_nbrs

Logical. If TRUE (default), sort K neighbors by ascending distance.

Value

A list with two elements:

knn_indices

Integer matrix (N x K). 1-based indices.

knn_distances

Numeric matrix (N x K). Distances.

See also

knn_from_pca, tcrdist_knn

Examples

# \donttest{
tcrs <- data.frame(
  va    = c("TRAV1-1*01", "TRAV1-1*01"),
  cdr3a = c("CAVRDSSYKLIF", "CAVRDSSYKLIF"),
  vb    = c("TRBV19*01", "TRBV19*01"),
  cdr3b = c("CASSIRSSYEQYF", "CASSIRSYEQYF"),
  stringsAsFactors = FALSE
)
D   <- tcrdist_matrix(tcrs, "human")
knn <- knn_from_matrix(D, K = 1L)
# }