makeAirrClone - Generate a airrClone object for lineage construction
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
object which serves as input for lineage reconstruction.
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", 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 )
- data.frame containing the AIRR or Change-O data for a clone. See Details for the list of required columns and their default values.
- name of the column containing sequence identifiers.
- name of the column containing observed DNA sequences. All sequences in this column must be multiple aligned.
- 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
- name of the column containing V-segment allele assignments. All entries in this column should be identical to the gene level.
- name of the column containing J-segment allele assignments. All entries in this column should be identical to the gene level.
- 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.
- name of the column containing the identifier for the clone. All entries in this column should be identical.
- character to use for masking and padding.
- maximum number of characters to mask at the leading and trailing
sequence ends. If
NULLthen 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.
TRUEpad the end of each sequence with
mask_charto make every sequence the same length.
- text annotation columns to retain and merge during duplicate removal.
- numeric annotation columns to retain and sum during duplicate removal.
- sequence annotation columns to retain and collapse during duplicate
removal. Note, this is distinct from the
germarguments, which contain the primary sequence data for the clone and should not be repeated in this argument.
TRUEadd an additional annotation column called
COLLAPSE_COUNTduring duplicate removal that indicates the number of sequences that were collapsed.
- passed on to
TRUE, report the numbers of input, discarded and output sequences; otherwise, process sequences silently.
- collapse identical sequences?
- if HL, include light chain information if available.
- name of heavy chain locus (default = “IGH”)
- name of the column containing cell assignment information
- name of the column containing locus information
- column ids to keep distinct during sequence collapse
- pad sequences to length mutliple three?
- randomize sequence order? Important if using PHYLIP
- assign CDR/FWR regions?
- Duplicate sequences in singleton clones to include them as trees?
A airrClone object containing the modified clone.
The input data.frame (
data) must columns for each of the required column name
Additional annotation columns specified in the
seq_fields arguments will be retained in the
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
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
cleanAlignment. It is highly likely we will change this system to a single
germline slot in the near future.
The airrClone object also contains vectors
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
data(ExampleAirr) airr_clone <- makeAirrClone(ExampleAirr[ExampleAirr$clone_id=="3184",])