Exporting clones

This function saves a csv file of clones (genes, amino acid, and nucleotide sequences) by barcodes. format determines the structure of the csv file - paired will export sequences by barcodes and include multiple chains, airr will export a data frame that is consistent with the AIRR format, and TCRMatch will export a data frame that has the TRB chain with count information.

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 to export the clones - "paired", "airr", or "TCRMatch".

group.by

The variable to use for grouping.

write.file

TRUE, save the file or FALSE, return a data.frame

dir

directory location to save the csv

file.name

the csv file name

Value

CSV file of the paired sequences.

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"))
exportClones(combined, 
             format = "paired")
} # }