| is_unproductive {clonotypeR} | R Documentation |
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.
is_unproductive(data)
data |
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.
Returns a logical vector, with one value per row in the original data.
Charles Plessy
clonotypes <- read_clonotypes(system.file('extdata', 'clonotypes.txt.gz', package = "clonotypeR"))
is_unproductive(clonotypes)