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Convert paired TCRs to a "thimble" data frame for Stitchr

create_thimble_df.Rd

[Experimental] This function creates a "thimble" data frame for use with the Stitchr Python package (https://jamieheather.github.io/stitchr/) to stitch together TCR nucleotide coding sequences. The resulting data frame can be written to a .tsv with write_stitchr_tsv().

Usage

create_thimble_df(
  df,
  preset = c("default", "none"),
  TCR_names = "TCR",
  exclude_non_functional = TRUE,
  remove_duplicates = TRUE,
  verbose = TRUE,
  Linker = NULL,
  Link_order = NULL,
  TRAC = NULL,
  TRBC = NULL,
  TRA_leader = NULL,
  TRB_leader = NULL,
  TRA_5_prime_seq = NULL,
  TRA_3_prime_seq = NULL,
  TRB_5_prime_seq = NULL,
  TRB_3_prime_seq = NULL
)

Arguments

df

a dataframe with paired TCRs.

preset

a preset for linker, link order, and TRAC/TRBC settings. The default ("default") setting uses "T2A" for the linker, "BA" for link order, "mTRAC\*01" for TRAC, and "mTRBC2\*01" for TRBC.

TCR_names

a vector of names for the TCRs. If a vector of length one, then TCR names will be "<TCR_names>_1", "<TCR_names>_2", ... , "<TCR_names>_N".

exclude_non_functional

whether to exclude TCRs with non-functional CDR3 sequences (default is TRUE).

remove_duplicates

whether to remove any duplicate TCRs (default is TRUE).

verbose

whether to print messages

Linker

the linker for TCRs (default "T2A")

the link order for TCRs (default "BA")

TRAC

TCR alpha chain constant region (default "mTRAC*01")

TRBC

TCR beta chain constant region (default "mTRBC2*01")

TRA_leader

(optional) An alternative leader sequence for the alpha chain. This can be either a specified gene entry in the pre-programmed IMGT data or alternatively a simple DNA string can be entered (e.g. ‘ATG’ for a minimal start codon in the absence of a leader sequence).

TRB_leader

(optional) An alternative leader sequence for the beta chain. This can be either a specified gene entry in the pre-programmed IMGT data or alternatively a simple DNA string can be entered (e.g. ‘ATG’ for a minimal start codon in the absence of a leader sequence).

TRA_5_prime_seq

Optional arbitrary sequence to be appended to the 5’ of the alpha chain.

TRA_3_prime_seq

Optional arbitrary sequence to be appended to the 3’ of the alpha chain.

TRB_5_prime_seq

Optional arbitrary sequence to be appended to the 5’ of the beta chain.

TRB_3_prime_seq

Optional arbitrary sequence to be appended to the 3’ of the beta chain.

Value

A data frame with TCRs properly formatted for use with Stitchr.

See also

Other stitchr: write_stitchr_tsv()