ContigCellDB {CellaRepertorium} | R Documentation |
Construct a ContigCellDB
ContigCellDB( contig_tbl, contig_pk, cell_tbl, cell_pk, cluster_tbl, cluster_pk = character(), equalize = TRUE ) ContigCellDB_10XVDJ( contig_tbl, contig_pk = c("barcode", "contig_id"), cell_pk = "barcode", ... )
contig_tbl |
a data frame of contigs, and additional fields describing their properties |
contig_pk |
character vector naming fields in |
cell_tbl |
a data frame of cell barcodes, and (optional) additional fields describing their properties |
cell_pk |
character vector naming fields in |
cluster_tbl |
A data frame that provide cluster assignments for each contig |
cluster_pk |
If |
equalize |
|
... |
passed to |
ContigCellDB
ContigCellDB_10XVDJ
: provide defaults that correspond to identifiers in 10X VDJ data
See $,ContigCellDB-method
for more on how to access and mutate slots.
See mutate_cdb()
and filter_cdb()
for endomorphic filtering/mutation methods
See split_cdb()
to split into a list, and rbind.ContigCellDB()
for the inverse operation.
data(contigs_qc) contigs_qc cdb = ContigCellDB(contigs_qc, contig_pk = c('barcode', 'pop', 'sample', 'contig_id'), cell_pk = c('barcode', 'pop', 'sample')) cdb # everything that was in contigs_qc cdb$contig_tbl # Only the cell_pk are included by default (until clustering/canonicalization) cdb$cell_tbl # Empty, since no cluster_pk was specified cdb$cluster_tbl # Keys cdb$contig_pk cdb$cell_pk cdb$cluster_pk