Read Adaptive Biotechnologies ImmunoSeq TSV file

Imports a beta-chain TCR repertoire from an Adaptive ImmunoSeq export file (TSV). Gene names are converted from Adaptive naming to IMGT format and optionally normalized to include an allele suffix.

Usage

read_adaptive(file, normalize_genes = TRUE)

Arguments

file: Character string. Path to an Adaptive ImmunoSeq TSV file.
normalize_genes: Logical. If TRUE (the default), gene names that lack an allele suffix (*XX) are appended with *01 after Adaptive-to-IMGT conversion.

Value

A data.frame with columns vb, jb, cdr3b, and optionally count. Gene names are in IMGT format. Rows with empty or NA CDR3 sequences are removed.

Details

Two column naming conventions are supported automatically:

Convention 1 (newer): vGeneName, jGeneName, aminoAcid, count
Convention 2 (older): v_resolved (or vFamilyName), j_resolved (or jFamilyName), aminoAcid, count / templates / reads

Examples

# \donttest{
# df <- read_adaptive("sample_immunoseq.tsv")
# head(df)
# }