Read AIRR Rearrangement TSV format

Reads a file in the AIRR Community Standard Rearrangement TSV format and returns a paired alpha-beta TCR data frame suitable for TCRrep. Each row in the AIRR format represents a single rearrangement; this function pairs alpha and beta chains by a shared identifier (typically cell_id).

Usage

read_airr(
  file,
  pair_by = "cell_id",
  productive_only = TRUE,
  normalize_genes = TRUE
)

Arguments

file

Character string. Path to an AIRR Rearrangement TSV file.

pair_by

Character string. Column name used to pair TRA and TRB rearrangements from the same cell. Defaults to "cell_id".

productive_only

Logical. If TRUE (default), only productive rearrangements are retained. The productive column may contain logical TRUE or character "T"/"TRUE".

normalize_genes

Logical. If TRUE (default), gene names lacking an allele suffix (e.g. "TRAV1-1") are appended with *01.

Value

A data.frame with columns cell_id, va, ja, cdr3a, vb, jb, cdr3b. Only cells with both a TRA and TRB rearrangement are included (inner join).

Details

Multi-value gene calls (comma-separated, e.g. "TRAV1-1*01,TRAV1-2*01") are resolved by taking the first listed allele.

See also

read_tcr_table, read_adaptive, read_10x

Examples

# \donttest{
# df <- read_airr("rearrangements.tsv")
# obj <- TCRrep(df, organism = "human")
# }