Determines if clonotype sequences are productive.
Data frame of clonotype sequences, or character vector describing a single clonotype, where the DNA sequence is available under the name “dna” and its translation available under the name “pep”.
Clonotypes are marked unproductive if the length of their DNA sequence is not a multiple of 3, or if they contain a stop codon, as indicated by an asterisk in the translated sequence.
ClonotypeR identifies V and J segments, isolates the DNA sequence between the conserved cystein and the FGxG motifs, and translates it. This functions verifies that this sequence is in frame and has no stop codon.
Logical vector, with one value per row in the original data.
clonotypes <- read_clonotypes(system.file('extdata', 'clonotypes.txt.gz', package = "clonotypeR")) is_unproductive(clonotypes)