formatClones

formatClones - Generate an ordered list of airrClone objects for lineage construction

Description¶

formatClones takes a data.frame or tibble with AIRR or Change-O style columns as input and masks gap positions, masks ragged ends, removes duplicates sequences, and merges annotations associated with duplicate sequences. If specified, it will un-merge duplicate sequences with different values specified in the trait option. It returns a list of airrClone objects ordered by number of sequences which serve as input for lineage reconstruction.

Usage¶

formatClones(
data,
seq = "sequence_alignment",
clone = "clone_id",
subclone = "subclone_id",
nproc = 1,
chain = "H",
heavy = "IGH",
cell = "cell_id",
locus = "locus",
minseq = 2,
split_light = FALSE,
majoronly = FALSE,
columns = NULL,
...
)

Arguments¶

data: data.frame containing the AIRR or Change-O data for a clone. See makeAirrClone for required columns and their defaults
seq: sequence alignment column name.
clone: name of the column containing the identifier for the clone. All entries in this column should be identical.
subclone: name of the column containing the identifier for the subclone.
nproc: number of cores to parallelize formating over.
chain: if HL, include light chain information if available.
heavy: name of heavy chain locus (default = “IGH”)
cell: name of the column containing cell assignment information
locus: name of the column containing locus information
minseq: minimum numbner of sequences per clone
split_light: split or lump subclones? See getSubclones.
majoronly: only return largest subclone and sequences without light chains
columns: additional data columns to include in output
…: additional arguments to pass to makeAirrClone

Value¶

A tibble of airrClone objects containing modified clones.

Details¶

This function is a wrapper for makeAirrClone. Also removes whitespace, ;, :, and = from ids

Examples¶

data(ExampleAirr)
# Select two clones, for demonstration purpose
sel <- c("3170", "3184")
clones <- formatClones(ExampleAirr[ExampleAirr$clone_id %in% sel,],trait="sample_id")