findSingleCellDuplicates - findSingleCellDuplicates

Description¶

Finds sequences that share the same identifier and sequence between groups.

Usage¶

findSingleCellDuplicates(
db,
fields,
cell_id = "cell_id",
seq = "sequence_alignment",
sequence_id = "sequence_id",
mode = c("sequences", "cells")
)

Arguments¶

db

data.frame with AIRR-format style columns.

fields

Columns in db, in addition to sample_id, that should be used to group sequences to be analyzed independently.

cell_id

column in db containing cell identifiers

seq

column in db containing sequences to be compared

sequence_id

column in db containing sequence identifiers

Value¶

A list with fields:

• dups: a data.frame with the column sc_duplicate with values TRUE/FALSE to indicate whether the the row corresponds to a duplicated entry.
• fields: a data.frame showing the input fields used
• cell_id: column in db containing cell identifiers
• seq: column in db containing sequence data
• sequence_id column in db containin sequence identifiers