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Assign alpha and beta chain group indices

Source: R/tcr_clumping.R
setup_tcr_groups.Rd

For each TCR in tcr_df, builds a composite key from the chain gene usage and CDR3 sequence, then assigns a 0-based group index so that identical chains share the same group. These groups are used for same-chain masking during neighbor search and Poisson testing.

Usage

setup_tcr_groups(tcr_df)

Arguments

tcr_df

A data.frame with at least the columns va, ja, cdr3a, vb, jb, cdr3b. Optional columns cdr3a_nucseq, cdr3b_nucseq, and subject_id are included in the key when present.

Value

A list with two elements:

agroups

Integer vector of length nrow(tcr_df). 0-based alpha-chain group indices.

bgroups

Integer vector of length nrow(tcr_df). 0-based beta-chain group indices.

See also

find_clumping

Examples

# \donttest{
tcr_df <- data.frame(
  va = c("TRAV1-1*01", "TRAV1-1*01", "TRAV12-2*01"),
  ja = c("TRAJ33*01", "TRAJ33*01", "TRAJ49*01"),
  cdr3a = c("CAVRDSSYKLIF", "CAVRDSSYKLIF", "CAVSANSGTYF"),
  vb = c("TRBV19*01", "TRBV19*01", "TRBV20-1*01"),
  jb = c("TRBJ2-7*01", "TRBJ2-7*01", "TRBJ1-1*01"),
  cdr3b = c("CASSIRSSYEQYF", "CASSIRSYEQYF", "CSARDRTGNTIYF"),
  stringsAsFactors = FALSE
)
groups <- setup_tcr_groups(tcr_df)
groups$agroups  # c(0, 0, 1)  (first two share alpha chain)
#> [1] 0 0 1
# }