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Export Clonal Data in Various Formats

Source: R/exportClones.R
exportClones.Rd

Exports clonal information (gene sequences, amino acids, nucleotides) from scRepertoire objects into a file or a data frame. The output format can be tailored for compatibility with different analysis workflows.

Usage

exportClones(
  input.data,
  format = "paired",
  group.by = NULL,
  write.file = TRUE,
  dir = NULL,
  file.name = "clones.csv"
)

Arguments

input.data

The product of combineTCR(), combineBCR(), or combineExpression().

format

The format for exporting clones. Options are: paired, airr, TCRMatch, tcrpheno, immunarch.

group.by

The variable in the metadata to use for grouping. If NULL, data will be grouped by the sample names.

write.file

If TRUE (default), saves the output to a CSV file. If FALSE, returns the data frame or list to the R environment.

dir

The directory where the output file will be saved. Defaults to the current working directory.

file.name

The name of the file to be saved.

Value

A data frame or list in the specified format, either returned to the R environment or saved as a CSV file.

Details

The format parameter determines the structure of the output:

  • paired: Exports a data frame where each row represents a barcode, with paired chain information (amino acid, nucleotide, genes) in separate columns.

  • airr: Exports a data frame that adheres to the Adaptive Immune Receptor Repertoire (AIRR) Community format, with each row representing a single receptor chain.

  • TCRMatch: Exports a data frame specifically for the TCRMatch algorithm, containing the TRB chain amino acid sequence and clonal frequency.

  • tcrpheno: Exports a data frame compatible with the tcrpheno pipeline, with TRA and TRB chains in separate columns.

  • immunarch: Exports a list containing a data frame and metadata formatted for use with the immunarch package.

Author

Jonathan Noonan, Nick Borcherding

Examples

if (FALSE) { # \dontrun{
#Making combined contig data
combined <- combineTCR(contig_list,
                       samples = c("P17B", "P17L", "P18B", "P18L",
                                   "P19B", "P19L", "P20B", "P20L"))

# Export as a paired data frame and save to a file
exportClones(combined, format = "paired", file.name = "paired_clones.csv")

# Return an AIRR-formatted data frame to the environment
airr_df <- exportClones(combined, format = "airr", write.file = FALSE)
} # }