generate_pseudobulk {CellaRepertorium} | R Documentation |
ContigCellDB
Tabulate contigs with a unique combination of class_keys
per total_keys
.
For instance, total_keys
might be a sample identifier, and class_keys
might
be the V- and J- gene identities. The idea is that this might mimic the data
generated in a bulk experiment.
generate_pseudobulk(ccdb, class_keys, total_keys, type = c("cell", "umi"))
ccdb |
|
class_keys |
|
total_keys |
|
type |
one of "cell" or "umi" |
This function is currently rather 10x-specific, in that it is assumed that columns barcode
and
umis
exist.
tibble
data(ccdb_ex) ccdb_ex = cluster_germline(ccdb_ex) pseudo = generate_pseudobulk(ccdb_ex, c('v_gene', 'j_gene', 'chain'), c('pop', 'sample'))