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 traits 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",
  subgroup = "clone_subgroup",
  id = "sequence_id",
  germ = "germline_alignment_d_mask",
  v_call = "v_call",
  j_call = "j_call",
  junc_len = "junction_length",
  mask_char = "N",
  max_mask = 0,
  pad_end = TRUE,
  text_fields = NULL,
  num_fields = NULL,
  seq_fields = NULL,
  add_count = TRUE,
  verbose = FALSE,
  collapse = TRUE,
  cell = "cell_id",
  locus = "locus",
  traits = NULL,
  mod3 = TRUE,
  randomize = TRUE,
  use_regions = TRUE,
  dup_singles = FALSE,
  nproc = 1,
  chain = "H",
  heavy = "IGH",
  filterstop = FALSE,
  minseq = 2,
  split_light = FALSE,
  light_traits = FALSE,
  majoronly = FALSE,
  columns = NULL
)

Value

A tibble of airrClone objects containing modified clones.

Arguments

data: data.frame containing the AIRR or Change-O data for a clone. See makeAirrClone for required columns and their defaults
seq: name of the column containing observed DNA sequences. All sequences in this column must be multiple aligned.
clone: name of the column containing the identifier for the clone. All entries in this column should be identical.
subgroup: name of the column containing the identifier for the subgroup.
id: name of the column containing sequence identifiers.
germ: name of the column containing germline DNA sequences. All entries in this column should be identical for any given clone, and they must be multiple aligned with the data in the seq column.
v_call: name of the column containing V-segment allele assignments. All entries in this column should be identical to the gene level.
j_call: name of the column containing J-segment allele assignments. All entries in this column should be identical to the gene level.
junc_len: name of the column containing the length of the junction as a numeric value. All entries in this column should be identical for any given clone.
mask_char: character to use for masking and padding.
max_mask: maximum number of characters to mask at the leading and trailing sequence ends. If NULL then the upper masking bound will be automatically determined from the maximum number of observed leading or trailing Ns amongst all sequences. If set to 0 (default) then masking will not be performed.
pad_end: if TRUE pad the end of each sequence with mask_char to make every sequence the same length.
text_fields: text annotation columns to retain and merge during duplicate removal.
num_fields: numeric annotation columns to retain and sum during duplicate removal.
seq_fields: sequence annotation columns to retain and collapse during duplicate removal. Note, this is distinct from the seq and germ arguments, which contain the primary sequence data for the clone and should not be repeated in this argument.
add_count: if TRUE add an additional annotation column called COLLAPSE_COUNT during duplicate removal that indicates the number of sequences that were collapsed.
verbose: passed on to collapseDuplicates. If TRUE, report the numbers of input, discarded and output sequences; otherwise, process sequences silently.
collapse: collapse identical sequences?
cell: name of the column containing cell assignment information
locus: name of the column containing locus information
traits: column ids to keep distinct during sequence collapse
mod3: pad sequences to length mutliple three?
randomize: randomize sequence order? Important if using PHYLIP
use_regions: assign CDR/FWR regions?
dup_singles: Duplicate sequences in singleton clones to include them as trees?
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")
filterstop: only use sequences that do not contain an in-frame stop codon
minseq: minimum number of sequences per clone
split_light: split or lump subgroups? See resolveLightChains.
light_traits: Include the traits from the light chain when concatenating and collapsing trees?
majoronly: only return largest subgroup and sequences without light chains
columns: additional data columns to include in output

Details

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

Examples

Run this code

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