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Pivot VDJ contig data to wide format

Source: R/preprocessing.R
pivot_VDJ.Rd

Converts VDJ contig annotation data from long format (one row per contig) to wide format (one row per cell barcode), creating composite TCR chain identifiers (TRA_1, TRA_2, TRB_1, TRB_2) from V gene, CDR3, and J gene.

Usage

pivot_VDJ(
  VDJ_data,
  sample_col = NULL,
  is_cell = FALSE,
  high_confidence = FALSE,
  productive = FALSE,
  full_length = FALSE,
  cdr3_col = "cdr3_nt",
  verbose = TRUE
)

Arguments

VDJ_data

A data frame of VDJ contig annotations in 10x Genomics format. Must contain columns: barcode, chain, v_gene, cdr3, j_gene, umis, and other standard 10x VDJ columns.

sample_col

Name of the column in VDJ_data to use as sample identifier. If NULL, all cells are assigned to a single sample called "Sample".

is_cell

Logical. If TRUE, filter to rows where is_cell == "true".

high_confidence

Logical. If TRUE, filter to rows where high_confidence == "true".

productive

Logical. If TRUE, filter to rows where productive == "true".

full_length

Logical. If TRUE, filter to rows where full_length == "true".

cdr3_col

Which CDR3 column to use for building the composite TCR chain identifier. Either "cdr3_nt" (nucleotide sequence, default) or "cdr3" (amino acid sequence).

verbose

Logical. If TRUE, print progress messages.

Value

A data frame in wide format with one row per cell barcode. Contains columns for sample, barcode, TCR chain identifiers (TRA_1, TRA_2, TRB_1, TRB_2), contig metadata, and individual chain component columns.