makeAirrClone: Generate a airrClone object for lineage construction

Description

makeAirrClone takes a data.frame 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. It returns a airrClone object which serves as input for lineage reconstruction.

Usage

makeAirrClone(
  data,
  id = "sequence_id",
  seq = "sequence_alignment",
  germ = "germline_alignment_d_mask",
  v_call = "v_call",
  j_call = "j_call",
  junc_len = "junction_length",
  clone = "clone_id",
  subgroup = "clone_subgroup",
  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,
  chain = "H",
  heavy = NULL,
  cell = "cell_id",
  locus = "locus",
  traits = NULL,
  mod3 = TRUE,
  randomize = TRUE,
  use_regions = TRUE,
  dup_singles = FALSE,
  light_traits = FALSE
)

Value

A airrClone object containing the modified clone.

Arguments

data: data.frame containing the AIRR or Change-O data for a clone. See Details for the list of required columns and their default values.
id: name of the column containing sequence identifiers.
seq: name of the column containing observed DNA sequences. All sequences in this column must be multiple aligned.
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.
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.
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?
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
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?
light_traits: Include the traits from the light chain when concatenating and collapsing trees?

Details

The input data.frame (data) must columns for each of the required column name arguments: id, seq, germ, v_call, j_call, junc_len, and clone. Additional annotation columns specified in the traits, text_fields, num_fields or seq_fields arguments will be retained in the data slot of the return object, but are not required. These options differ by their behavior among collapsed sequences. Identical sequences that differ by any values specified in the traits option will be kept distinct. Identical sequences that differ only by values in the num_fields option will be collapsed and the values of their num_fields columns will be added together. Similar behavior occurs with text_fields but the unique values will concatenated with a comma.

The default columns are IMGT-gapped sequence columns, but this is not a requirement. However, all sequences (both observed and germline) must be multiple aligned using some scheme for both proper duplicate removal and lineage reconstruction.

The value for the germline sequence, V-segment gene call, J-segment gene call, junction length, and clone identifier are determined from the first entry in the germ, v_call, j_call, junc_len and clone columns, respectively. For any given clone, each value in these columns should be identical.

To allow for cases where heavy and light chains are used, this function returns three sequence columns for heavy chains (sequence), light chain (lsequence, empty if none available), and concatenated heavy+light chain (hlsequence). These contain sequences in alignment with germline, lgermline, and hlgermline slots, respectively. The sequence column used for build trees is specified in the phylo_seq slot. Importantly, this column is also the sequence column that also has uninformative columns removed by cleanAlignment. It is highly likely we will change this system to a single sequence and germline slot in the near future.

The airrClone object also contains vectors locus, region, and numbers, which contain the locus, IMGT region, and IMGT number for each position in the sequence column specified in phylo_seq. If IMGT-gapped sequences are not supplied, this will likely result in an error. Specify use_regions=FALSE if not using IMGT-gapped sequences

Examples

Run this code

data(ExampleAirr)
airr_clone <- makeAirrClone(ExampleAirr[ExampleAirr$clone_id=="3184",])