annotateDB: Use reference database to annotate cdr3 sequences
In ncborcherding/Trex: Methods for TCR single-cell embedding
annotateDB R Documentation
Use reference database to annotate cdr3 sequences
Description
Use meta database of cdr3 sequences as a reference to
cdr3 aa sequence of the single cells.
Usage
annotateDB(sc, chains = "TRB", edit.distance = 0)
Arguments
sc
Single Cell Object in Seurat or Single-Cell Experiment format
chains
TCR chain to use - TRA or TRB
edit.distance
Number of amino acid residues different than reference
using Levenshtein distance. Distances of <= 2 are optimal.
Value
Seurat or SingleCellExperiment object with epitope information
added to the metadata.
Examples
trex_example <- annotateDB(trex_example,
chains = "TRB")
ncborcherding/Trex documentation built on Nov. 4, 2024, 10:31 p.m.
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| annotateDB | R Documentation |
Use reference database to annotate cdr3 sequences
Description
Use meta database of cdr3 sequences as a reference to cdr3 aa sequence of the single cells.
Usage
annotateDB(sc, chains = "TRB", edit.distance = 0)
Arguments
sc |
Single Cell Object in Seurat or Single-Cell Experiment format |
chains |
TCR chain to use - TRA or TRB |
edit.distance |
Number of amino acid residues different than reference using Levenshtein distance. Distances of <= 2 are optimal. |
Value
Seurat or SingleCellExperiment object with epitope information added to the metadata.
Examples
trex_example <- annotateDB(trex_example,
chains = "TRB")
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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