is_unproductive: Determines if clonotype sequences are productive.
In charles-plessy/clonotypeR.old: High throughput analysis of T cell antigen receptor sequences
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
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.
Usage
1
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”.
Details
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.
Value
Returns a logical vector, with one value per row in the original data.
Author(s)
Charles Plessy
See Also
Examples
1
2
clonotypes <- read_clonotypes(system.file('extdata', 'clonotypes.txt.gz', package = "clonotypeR"))
is_unproductive(clonotypes)
charles-plessy/clonotypeR.old documentation built on May 13, 2019, 3:31 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
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.
Usage
1 |
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”. |
Details
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.
Value
Returns a logical vector, with one value per row in the original data.
Author(s)
Charles Plessy
See Also
Examples
1 2 | clonotypes <- read_clonotypes(system.file('extdata', 'clonotypes.txt.gz', package = "clonotypeR"))
is_unproductive(clonotypes)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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