is_unproductive: is_unproductive

In clonotypeR: High throughput analysis of T cell antigen receptor sequences

Description

Determines if clonotype sequences are productive.

Usage

is_unproductive(data)

Arguments

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.

Details

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.

Value

Logical vector, with one value per row in the original data.

See Also

read_clonotypes

Examples

clonotypes <- read_clonotypes(system.file('extdata', 'clonotypes.txt.gz', package = "clonotypeR"))
is_unproductive(clonotypes)

clonotypeR documentation built on Nov. 8, 2020, 6:51 p.m.