generate_pseudobulk {CellaRepertorium}

R Documentation

Generate "pseudobulk" data from a ContigCellDB

Description

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.

Usage

generate_pseudobulk(ccdb, class_keys, total_keys, type = c("cell", "umi"))

Arguments

ccdb	ContigCellDB()
class_keys	character naming fields in contig_tbl that define unique classes of the repertoire
total_keys	character naming fields to be conditioned upon when calculating the total.
type	one of "cell" or "umi"

Details

This function is currently rather 10x-specific, in that it is assumed that columns barcode and umis exist.

Value

tibble

Examples

data(ccdb_ex)
ccdb_ex = cluster_germline(ccdb_ex)
pseudo = generate_pseudobulk(ccdb_ex, c('v_gene', 'j_gene', 'chain'), c('pop', 'sample'))

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