| extdata {clonotypeR} | R Documentation |
Data frame derived from Table 1 of Yassai et al., 2009, to construct clonotype names.
V_after_C: sequence of the V segments after their conserved cystein.
J_before_FGxG: sequence of the J segments before their conserved FGxG motif.
codon_ids: data frame derived from Table 1 of Yassai et al., 2009, to construct clonotype names.
The V_after_C and J_before_FGxG tables are, generated from the mouse reference data with the
command: make refresh-data in the source repository of clonotypeR.
codon_ids:
codon |
Nucleotide triplet. |
aminoacid |
Single-letter amino acid abbreviation (“O” for stop). |
id |
ID numbers assigned to the codons for each amino acids. |
J_before_FGxG:
row name |
J segment name, for instance “TRAJ61”. |
sequence |
Sequence of the nucleic acids preceding the first codon of the conserved FGxG motif. |
V_after_C:
row name |
V segment name, for instance “TRAV1”. |
sequence |
Sequence of the nucleic acids following the codon of the conserved cysteine. |
A clonotype nomenclature for T cell receptors. Maryam B. Yassai, Yuri N. Naumov, Elena N. Naumova and Jack Gorski Immunogenetics, 2009, Volume 61, Number 7, Pages 493-502
V_after_C <- read.table(system.file('extdata', 'V_after_C.txt.gz', package = "clonotypeR"), stringsAsFactors=FALSE)
J_before_FGxG <- read.table(system.file('extdata', 'J_before_FGxG.txt.gz', package = "clonotypeR"), stringsAsFactors=FALSE)
codon_ids <- read.table(system.file('extdata', 'codon_ids.txt.gz', package = "clonotypeR"), header=TRUE, row.names=1)