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.
ig_chain_recode(tbl)
tcr_chain_recode(tbl)
enumerate_pairing(ccdb, chain_key = "chain", chain_recode_fun = NULL)output from enumerate_pairing containing TRA/TRB or IGH/IHK/IHL columns
ContigCellDB
character naming the field in the contig_tbl identifying chain
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.
a tibble keyed by cells.
ig_chain_recode: Recode a table with IG chains
tcr_chain_recode: Recode a table with TCR chains
data(ccdb_ex)
enumerate_pairing(ccdb_ex)
#> # A tibble: 832 × 6
#> pop sample barcode TRA TRB raw_chain_type
#> <chr> <chr> <chr> <dbl> <dbl> <chr>
#> 1 b6 4 AAAGTAGTCGCGCCAA-1 1 2 TRA_TRB_TRB
#> 2 b6 4 AACCATGCATTTGCCC-1 1 0 TRA
#> 3 b6 4 AACTGGTGTCTGATCA-1 1 1 TRA_TRB
#> 4 b6 4 AAGCCGCAGTAAGTAC-1 0 1 TRB
#> 5 b6 4 AAGTCTGGTTCAACCA-1 1 1 TRA_TRB
#> 6 b6 4 ACACCAAAGTCCAGGA-1 1 1 TRA_TRB
#> 7 b6 4 ACATGGTAGTGTTTGC-1 1 1 TRA_TRB
#> 8 b6 4 ACCCACTTCCACGACG-1 1 1 TRA_TRB
#> 9 b6 4 ACGCCAGGTCCGAATT-1 0 1 TRB
#> 10 b6 4 ACGCCAGTCCAATGGT-1 0 1 TRB
#> # … with 822 more rows
enumerate_pairing(ccdb_ex, chain_recode_fun = 'guess')
#> # A tibble: 832 × 8
#> pop sample barcode TRA TRB raw_chain_type pairing canonical
#> <chr> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr>
#> 1 b6 4 AAAGTAGTCGCGCCAA-1 1 2 TRA_TRB_TRB paired double-be…
#> 2 b6 4 AACCATGCATTTGCCC-1 1 0 TRA alpha classical
#> 3 b6 4 AACTGGTGTCTGATCA-1 1 1 TRA_TRB paired classical
#> 4 b6 4 AAGCCGCAGTAAGTAC-1 0 1 TRB beta classical
#> 5 b6 4 AAGTCTGGTTCAACCA-1 1 1 TRA_TRB paired classical
#> 6 b6 4 ACACCAAAGTCCAGGA-1 1 1 TRA_TRB paired classical
#> 7 b6 4 ACATGGTAGTGTTTGC-1 1 1 TRA_TRB paired classical
#> 8 b6 4 ACCCACTTCCACGACG-1 1 1 TRA_TRB paired classical
#> 9 b6 4 ACGCCAGGTCCGAATT-1 0 1 TRB beta classical
#> 10 b6 4 ACGCCAGTCCAATGGT-1 0 1 TRB beta classical
#> # … with 822 more rows