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Validate and correct TCR chain data

Source: R/preprocessing.R
validate_TCR.Rd

Validates TCR chain columns (TRA_1, TRA_2, TRB_1, TRB_2) by:

  • Checking V-CDR3-J format validity

  • Reordering chains into the canonical V_CDR3_J format,

  • Removing duplicate alleles (where allele 1 equals allele 2)

  • Swapping alleles when allele 2 is defined but allele 1 is missing.

Usage

validate_TCR(TCR_data, remove_invalid_VDJ = FALSE, verbose = TRUE)

Arguments

TCR_data

A data frame with columns TRA_1, TRA_2, TRB_1, TRB_2 containing TCR chain identifiers in V_CDR3_J format.

remove_invalid_VDJ

Logical. If TRUE, set invalid VDJ sequences (those with missing V, CDR3, or J components) to NA. If FALSE, keep them as-is and flag them.

verbose

Logical. If TRUE, print progress messages.

Value

The input data frame with corrected TCR chain columns and additional logical columns (TRA_1.invalid, TRA_2.invalid, TRB_1.invalid, TRB_2.invalid) indicating which chains had invalid VDJ format.