align_imgt_ref_to_TCR_seq: Align IMGTs reference sequences to your TCR sequence

In Close-your-eyes/igsc: Immunoglobolin sequences from scRNAseq

Align IMGTs reference sequences to your TCR sequence

Description

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.

Usage

align_imgt_ref_to_TCR_seq(
  chain,
  TCR,
  cl_long,
  imgt_ref,
  sequence_col = "consensus_seq",
  C_allele = NULL,
  type = "local",
  ...
)

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
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
type	type of alignment
...	arguments to MultiplePairwiseAlignmentsToOneSubject
cl_wide	clonotype data frame wide format

Value

a list

Close-your-eyes/igsc documentation built on Jan. 28, 2024, 10:28 p.m.