hierarchicalClones: Hierarchical clustering method for clonal partitioning

Description

hierarchicalClones provides a hierarchical agglomerative clustering approach to infer clonal relationships in high-throughput Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) data. This approach clusters B or T cell receptor sequences based on junction region sequence similarity within partitions that share the same V gene, J gene, and junction length, allowing for ambiguous V or J gene annotations.

Usage

hierarchicalClones(
  db,
  threshold,
  method = c("nt", "aa"),
  linkage = c("single", "average", "complete"),
  normalize = c("len", "none"),
  junction = "junction",
  v_call = "v_call",
  j_call = "j_call",
  clone = "clone_id",
  fields = NULL,
  cell_id = NULL,
  locus = "locus",
  only_heavy = TRUE,
  split_light = TRUE,
  first = FALSE,
  cdr3 = FALSE,
  mod3 = FALSE,
  max_n = 0,
  nproc = 1,
  verbose = FALSE,
  log = NULL,
  summarize_clones = TRUE
)

Value

If summarize_clones=TRUE (default) a ScoperClones object is returned that includes the clonal assignment summary information and a modified input db in the db slot that contains clonal identifiers in the specified clone column. If summarize_clones=FALSE modified data.frame is returned with clone identifiers in the specified clone column.

Arguments

db: data.frame containing sequence data.
threshold: numeric scalar where the tree should be cut (the distance threshold for clonal grouping).
method: one of the "nt" for nucleotide based clustering or "aa" for amino acid based clustering.
linkage: available linkage are "single", "average", and "complete".
normalize: method of normalization. The default is "len", which divides the distance by the length of the sequence group. If "none" then no normalization if performed.
junction: character name of the column containing junction sequences. Also used to determine sequence length for grouping.
v_call: name of the column containing the V-segment allele calls.
j_call: name of the column containing the J-segment allele calls.
clone: output column name containing the clonal cluster identifiers.
fields: character vector of additional columns to use for grouping. Sequences with disjoint values in the specified fields will be classified as separate clones.
cell_id: name of the column containing cell identifiers or barcodes. If specified, grouping will be performed in single-cell mode with the behavior governed by the locus and only_heavy arguments. If set to NULL then the bulk sequencing data is assumed.
locus: name of the column containing locus information. Only applicable to single-cell data. Ignored if cell_id=NULL.
only_heavy: use only the IGH (BCR) or TRB/TRD (TCR) sequences for grouping. Only applicable to single-cell data. Ignored if cell_id=NULL.
split_light: split clones by light chains. Ignored if cell_id=NULL.
first: specifies how to handle multiple V(D)J assignments for initial grouping. If TRUE only the first call of the gene assignments is used. If FALSE the union of ambiguous gene assignments is used to group all sequences with any overlapping gene calls.
cdr3: if TRUE removes 3 nucleotides from both ends of "junction" prior to clustering (converts IMGT junction to CDR3 region). If TRUE this will also remove records with a junction length less than 7 nucleotides.
mod3: if TRUE removes records with a junction length that is not divisible by 3 in nucleotide space.
max_n: The maximum number of degenerate characters to permit in the junction sequence before excluding the record from clonal assignment. Note, with linkage="single" non-informative positions can create artifactual links between unrelated sequences. Use with caution. Default is set to be zero. Set it as "NULL" for no action.
nproc: number of cores to distribute the function over.
verbose: if TRUE prints out a summary of each step cloning process. if FALSE (default) process cloning silently.
log: output path and filename to save the verbose log. The input file directory is used if path is not specified. The default is NULL for no action.
summarize_clones: if TRUE performs a series of analysis to assess the clonal landscape and returns a ScoperClones object. If FALSE then a modified input db is returned. When grouping by fields, summarize_clones should be FALSE.

Single-cell data

To invoke single-cell mode the cell_id argument must be specified and the locus column must be correct. Otherwise, clustering will be performed with bulk sequencing assumptions, using all input sequences regardless of the values in the locus column.

Values in the locus column must be one of c("IGH", "IGI", "IGK", "IGL") for BCR or c("TRA", "TRB", "TRD", "TRG") for TCR sequences. Otherwise, the operation will exit and return an error message.

Under single-cell mode with paired-chain sequences, there is a choice of whether grouping should be done by (a) using IGH (BCR) or TRB/TRD (TCR) sequences only or (b) using IGH plus IGK/IGL (BCR) or TRB/TRD plus TRA/TRG (TCR) sequences. This is governed by the only_heavy argument. There is also choice as to whether inferred clones should be split by the light/short chain (IGK, IGL, TRA, TRG) following heavy/long chain clustering, which is governed by the split_light argument.

In single-cell mode, clonal clustering will not be performed on data where cells are assigned multiple heavy/long chain sequences (IGH, TRB, TRD). If observed, the operation will exit and return an error message. Cells that lack a heavy/long chain sequence (i.e., cells with light/short chains only) will be assigned a clone_id of NA.

Examples

Run this code

# Find clonal groups
results <- hierarchicalClones(ExampleDb, threshold=0.15)

# Retrieve modified input data with clonal clustering identifiers
df <- as.data.frame(results)

# Plot clonal summaries
plot(results, binwidth=0.02)