makeChangeoClone - Generate a ChangeoClone object for lineage construction
Description¶
makeChangeoClone
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 ChangeoClone
object which serves as input for lineage reconstruction.
Usage¶
makeChangeoClone(
data,
id = "sequence_id",
seq = "sequence_alignment",
germ = "germline_alignment",
v_call = "v_call",
j_call = "j_call",
junc_len = "junction_length",
clone = "clone_id",
mask_char = "N",
max_mask = 0,
pad_end = FALSE,
text_fields = NULL,
num_fields = NULL,
seq_fields = NULL,
add_count = TRUE,
verbose = FALSE
)
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.
- 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 to0
(default) then masking will not be performed. - pad_end
- if
TRUE
pad the end of each sequence withmask_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
andgerm
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 calledcollapse_count
during duplicate removal that indicates the number of sequences that were collapsed. - verbose
- passed on to
collapseDuplicates
. IfTRUE
, report the numbers of input, discarded and output sequences; otherwise, process sequences silently.
Value¶
A ChangeoClone object containing the modified clone.
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
. The default values are as follows:
id = "sequence_id"
: unique sequence identifier.seq = "sequence_alignment"
: IMGT-gapped sample sequence.germ = "germline_alignment"
: IMGT-gapped germline sequence.v_call = "v_call"
: V segment allele call.j_call = "j_call"
: J segment allele call.junc_len = "junction_length"
: junction sequence length.clone = "clone_id"
: clone identifier.
Additional annotation columns specified in the text_fields
, num_fields
or seq_fields
arguments will be retained in the data
slot of the return
object, but are not required. If the input data.frame data
already contains a
column named sequence
, which is not used as the seq
argument, then that
column will not be retained.
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.
Examples¶
# Example data
db <- data.frame(sequence_id=LETTERS[1:4],
sequence_alignment=c("CCCCTGGG", "CCCCTGGN", "NAACTGGN", "NNNCTGNN"),
germline_alignment="CCCCAGGG",
v_call="Homsap IGKV1-39*01 F",
j_call="Homsap IGKJ5*01 F",
junction_length=2,
clone_id=1,
c_call=c("IGHM", "IGHG", "IGHG", "IGHA"),
duplicate_count=1:4,
stringsAsFactors=FALSE)
# Without end masking
makeChangeoClone(db, text_fields="c_call", num_fields="duplicate_count")
Error in makeChangeoClone(db, text_fields = “c_call”, num_fields = “duplicate_count”): The column locus was not found
# With end masking
makeChangeoClone(db, max_mask=3, text_fields="c_call", num_fields="duplicate_count")
Error in makeChangeoClone(db, max_mask = 3, text_fields = “c_call”, num_fields = “duplicate_count”): The column locus was not found
See also¶
Executes in order maskSeqGaps, maskSeqEnds, padSeqEnds, and collapseDuplicates. Returns a ChangeoClone object which serves as input to buildPhylipLineage.