add_cdr3_anchors: Add CDR3 anchor residues

In obrzts/BLscore: Clustering Similar TCRs Likely Recognizing Same Epitope

Add CDR3 anchor residues

Description

Construct full TCR junction sequence by adding conservative anchor residues (C and F/W) to CDR3 sequence.

Usage

add_cdr3_anchors(sequence_df, chains, species = "human")

Arguments

sequence_df	A data.frame containing CDR3 sequences and J genes. Columns must be named cdr3_beta and j_beta and/or cdr3_alpha and j_alpha.
chains	Which chains to process. "B" for beta chain only, "A" for alpha, "AB" for both.
species	From which species are the sequences. Currently only human and mouse are supported.

Value

Same data.frame as input with additional columns junction_beta and/or jucntion_alpha

Examples

# make example table without anchor residues
df <- example_TCR_df
df$cdr3_beta <- substr(df$junction_beta, 2, nchar(df$junction_beta) - 2)

# generate column with beta chain junction sequence
df <- add_cdr3_anchors(df, "B", species="human")

obrzts/BLscore documentation built on Nov. 21, 2024, 4:28 a.m.