Read a delimited file containing TCR repertoire data

Reads a CSV or TSV file of TCR clonotypes and returns a data.frame with tcrdistR canonical column names (va, cdr3a, vb, cdr3b, and optionally ja, jb). Common naming conventions (e.g. tcrdist3/DASH format) are auto-detected when col_map is not provided.

Usage

read_tcr_table(file, col_map = NULL, sep = "\t", normalize_genes = TRUE, ...)

Arguments

file

Character string. Path to a delimited text file.

col_map

A named list mapping tcrdistR canonical column names to the column names used in file. For example, list(va = "v_a_gene", cdr3a = "cdr3_a_aa"). If NULL (the default), the function attempts to auto-detect the naming pattern.

sep

Character. Field separator passed to read.delim. Defaults to "\t" (tab-separated).

normalize_genes

Logical. If TRUE (default), V and J gene names that lack an allele suffix (e.g. TRAV1-1) are normalised by appending *01.

...

Additional arguments passed to read.delim.

Value

A data.frame with tcrdistR canonical column names. All gene and CDR3 columns are character vectors (never factors).

See also

read_airr, read_adaptive, read_10x, TCRrep

Examples

# \donttest{
# Read a tcrdist3-style TSV file
# df <- read_tcr_table("dash_human.tsv")

# Read a CSV with custom column mapping
# df <- read_tcr_table("my_data.csv", sep = ",",
#     col_map = list(va = "V_alpha", cdr3a = "CDR3_alpha",
#                    vb = "V_beta",  cdr3b = "CDR3_beta"))
# }