match_TCR_chains: Match the TCR junctions and (optionally) V and J genes...

In mjdufort/TCRtools: Helper functions for analyzing TCR sequence data from single-cell RNA-seq

Description

Determine matching TCR chain sequences among a set of single-cell TCR sequences. By default, chains are matched by the junction, V gene, and J gene. Matching by V and/or J genes can be disabled.

Usage

match_TCR_chains(
     tcrs,
     id_col="libid",
     junction_col="junction",
     match_V_gene=TRUE, match_J_gene=TRUE,
     V_gene_col="v_gene", J_gene_col="j_gene")

Arguments

tcrs	a data frame containing the TCR sequences. Should include an identifier column, plus columns for junction and optionally the V and J genes.
id_col	number or name of the column containing the identifiers
junction_col	number or name of the column containing the TCR junctions
match_V_gene, match_J_gene	logical, whether to include the V/J genes when matching TCR chains. Default to TRUE. If set to FALSE, the V/J gene identities are ignored when matching chains.
V_gene_col, J_gene_col	number or name of the columns containing the V and J genes. Ignored if match_V_gene and/or match_J_gene are set to FALSE.

Value

A data frame containing the TCR chain information (junction and optionally V and J genes) and the identifiers for the two cells with matching chains. Identifier column names in the returned data frame are "tcr1" and "tcr2".

mjdufort/TCRtools documentation built on Sept. 12, 2021, 7:11 p.m.