annotate_cdr3: Annotate CDR3 sequences stored in colData(sce)$vdj based on a...

In keshav-motwani/scanalysis: Multi-Sample Visualization and Immune Repertoire Analysis Utilities for Single-Cell Data

Description

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

Usage

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

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keshav-motwani/scanalysis documentation built on Feb. 4, 2021, 2:21 a.m.