formatClones {dowser}

R Documentation

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

Details

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

Value

A tibble of airrClone objects containing modified clones.

See Also

Executes in order makeAirrClone. Returns a tibble of airrClone objects which serve as input to getTrees and findSwitches.

Examples

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

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