enumerate_pairing: Categorize the pairing present in a cell

In CellaRepertorium: Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)

Description

For each cell (defined by ccdb$cell_pk) count the number of each level of chain_key occurs, and cross tabulate. Also for each cell, paste together all values chain_key. Return a tibble, keyed by cells that includes the counts of the chains, the raw_chain_type and any additional output from running chain_recode_fun.

Usage

ig_chain_recode(tbl)

tcr_chain_recode(tbl)

enumerate_pairing(ccdb, chain_key = "chain", chain_recode_fun = NULL)

Arguments

tbl	output from enumerate_pairing containing TRA/TRB or IGH/IHK/IHL columns
ccdb	ContigCellDB
chain_key	character naming the field in the contig_tbl identifying chain
chain_recode_fun	a function that operates on the output of this function that further reduces the chain combinations to some other summary. Set to 'guess' to apply functions that may work for 10X data or NULL to skip. See CellaRepertorium::tcr_chain_recode for an example.

Value

a tibble keyed by cells.

Functions

• ig_chain_recode: Recode a table with IG chains

• tcr_chain_recode: Recode a table with TCR chains

Examples

data(ccdb_ex)
enumerate_pairing(ccdb_ex)
enumerate_pairing(ccdb_ex, chain_recode_fun = 'guess')

CellaRepertorium documentation built on Nov. 8, 2020, 7:48 p.m.