Align IMGTs reference sequences to your TCR sequence — align_imgt_ref_to_TCR

With Biostrings::pairwiseAlignment() the borders of the V(D)J-segments in your TCR sequence can be determined. The sequence within these border may then be used for further steps. In case of mouse, IMGT gene segments from Mus musculus are preferred.

align_imgt_ref_to_TCR_seq(
  chain,
  TCR,
  cl_long,
  cl_wide,
  imgt_ref,
  sequence_col = "consensus_seq_cr",
  C_allele
)

Arguments

chain	character which TCR chain to align, currently only TRA and TRB
TCR	a named vector; which of your TCRs to align, the name indicates which column name of cl_long to use, the value indicates what to look for in that column
cl_long	clonotype data frame long format
cl_wide	clonotype data frame wide format
imgt_ref	the prepared data.frame of IMGT references
sequence_col	name of the column to pull sequences from
C_allele	optional name of the constant allele to use for the alignment, must be the entry in the "Allele"-column of the imgt_ref data frame

Value

a list

Examples

if (FALSE) {

}