Annotate CDR3 sequences stored in colData(sce)$vdj based on a reference dataset (for example, Ag-specific data)

Source: R/annotate_cdr3.R

Annotate CDR3 sequences stored in colData(sce)$vdj based on a reference dataset (for example, Ag-specific data)

annotate_cdr3(
  sce,
  reference,
  reference_cdr3_column,
  reference_annotation_column,
  chain_match = "TRB",
  max_dist = 1,
  method = "hamming"
)

Arguments

sce

SingleCellExperiment object
reference

reference dataset for use in annotating query sequences
reference_cdr3_column

column in reference which contains the CDR3 region
reference_annotation_column

column in reference to annotate onto query dataset
chain_match

chain(s) to match (for example, c("TRA", "TRB"))
max_dist

maximum distance to allow between query and reference sequence
method

distance metric- one of "osa", "lv", "dl", "hamming", "lcs", "qgram", "cosine", "jaccard", "jw", "soundex"

Value

SingleCellExperiment object with additional column with the same name as reference_annotation_column

Examples

NULL
#> NULL