(Re)clonotype a VDJ object using cellranger's enclone tool

Source: R/VDJ_call_enclone.R

Calls recon to clonotype a VDJ object given a VDJ.directory (with sample folders which should include the all_contig_annotations.json file) - outputs a new VDJ with updated clonotype_id, clonotype_id_10x, and clonotype_frequency columns

VDJ_call_enclone(
  VDJ,
  VDJ.directory,
  global.clonotype,
  samples.to.clonotype,
  samples.to.combine,
  same.origin,
  output.format,
  operating.system,
  parallel
)

Arguments

VDJ

VDJ or VDJ.GEX.matrix[[1]] object, as obtained from the VDJ_GEX_matrix function in Platypus.

VDJ.directory

string - directory for the VDJ data, should be the main folder which includes the individual sample folders (each with the all_contig_annotations.json file that is used by enclone)

global.clonotype

bool - if T, will use clonotype definitions irrespective of samples. Must also be T is you wish to merge clonotypes from two specific (which should be specified in the samples.to.combine parameter)

samples.to.clonotype

- vector - lists the samples names which should be clonotyped. The unspecified samples will keep their old clonotype defintions.

samples.to.combine

- vector or list of vectors - lists the samples which you wish to have their clonotypes merged (e.g., c('s1','s2') to only merge the first 2 samples, or list(c('s1','s3'), c('s2', 's4')) to merge the first and third, second and fourth, respectively). global.clonotype must be set to T!

same.origin

bool - if the merged samples come from the same donor, with the same or with different origins. If two datasets come from the same origin, enclone will filter to remove certain artifacts.

output.format

string - 'vgm' to output a VGM-specific VDJ dataframe (all samples in the same dataframe).

operating.system

string - operating system on which enclone will be run. 'Windows' for Windows, 'Linux' for Linux, 'Darwin' for MacOS.

parallel

bool - if T, the program will be executed in parallel, on no. cores = max. available cores - 1.

Value

Reclonotyped VDJ object using the enclone software and 10x-specific clonotype deifinition.

Examples

if (FALSE) {
VDJ_call_enclone(vdj, VDJ.directory, samples.to.combine = c('s1', 's2', 's3'), global.clonotype = T)
}