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Radius-based TCRdist neighbor search with optional group masking

Source: R/wrappers_neighbors.R
tcrdist_radius_neighbors.Rd

For each of the N input TCRs, finds all other TCRs within radius TCRdist distance. TCRs sharing the same agroups or bgroups value are excluded (same-group masking).

Usage

tcrdist_radius_neighbors(
  tcrs,
  organism,
  radius,
  agroups = NULL,
  bgroups = NULL,
  components = "all",
  weight_cdr3 = WEIGHT_CDR3_REGION,
  gap_penalty_cdr3 = GAP_PENALTY_CDR3_REGION
)

Arguments

tcrs

A data.frame with at least the following columns:

va

Character. Alpha-chain V-gene allele.

cdr3a

Character. Alpha-chain CDR3 amino acid sequence.

vb

Character. Beta-chain V-gene allele.

cdr3b

Character. Beta-chain CDR3 amino acid sequence.

organism

Character string. Organism key, e.g. "human".

radius

Numeric. Search radius (inclusive). Pairs with distance <= radius are returned. Must be >= 0.

agroups

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

bgroups

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

components

Character. Which distance components to include. See tcrdist_matrix for details. Default "all".

weight_cdr3

Integer. CDR3 distance weight. Defaults to WEIGHT_CDR3_REGION (3L).

gap_penalty_cdr3

Integer. CDR3 gap penalty. Defaults to GAP_PENALTY_CDR3_REGION (12L).

Value

A list of length N. Each element [[i]] is a list with:

indices

Integer vector. 1-based indices of neighbors within radius.

distances

Numeric vector. Corresponding distances.

See also

tcrdist_knn, find_clumping

Examples

# \donttest{
tcrs <- data.frame(
  va    = c("TRAV1-1*01", "TRAV1-1*01", "TRAV12-2*01"),
  cdr3a = c("CAVRDSSYKLIF", "CAVRDSSYKLIF", "CAVSANSGTYF"),
  vb    = c("TRBV19*01", "TRBV19*01", "TRBV20-1*01"),
  cdr3b = c("CASSIRSSYEQYF", "CASSIRSYEQYF", "CSARDRTGNTIYF"),
  stringsAsFactors = FALSE
)
nbrs <- tcrdist_radius_neighbors(tcrs, "human", radius = 50)
# }