exportClones: Exporting clones

In ncborcherding/scRepertoire: A toolkit for single-cell immune receptor profiling

Exporting clones

Description

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.

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 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(s)

Jonathan Noonan, Nick Borcherding

Examples

## Not run: 
#Making combined contig data
combined <- combineTCR(contig_list, 
                        samples = c("P17B", "P17L", "P18B", "P18L", 
                                    "P19B","P19L", "P20B", "P20L"))
exportClones(combined, 
             format = "paired")

## End(Not run)
                                   

ncborcherding/scRepertoire documentation built on Nov. 5, 2024, 2:05 p.m.