spectralClones - Spectral clustering method for clonal partitioning

Description

spectralClones provides an unsupervised spectral 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 and shared mutations within partitions that share the same V gene, J gene, and junction length, allowing for ambiguous V or J gene annotations.

Usage

spectralClones(
db,
method = c("novj", "vj"),
germline = "germline_alignment",
sequence = "sequence_alignment",
junction = "junction",
v_call = "v_call",
j_call = "j_call",
clone = "clone_id",
cell_id = NULL,
locus = "locus",
only_heavy = TRUE,
split_light = TRUE,
targeting_model = NULL,
len_limit = NULL,
first = FALSE,
cdr3 = FALSE,
mod3 = FALSE,
max_n = 0,
threshold = NULL,
base_sim = 0.95,
iter_max = 1000,
nstart = 1000,
nproc = 1,
verbose = FALSE,
log = NULL,
summarize_clones = TRUE
)

Arguments

db
data.frame containing sequence data.
method
one of the "novj" or "vj". See Details for description.
germline
character name of the column containing the germline or reference sequence.
sequence
character name of the column containing input sequences.
junction
character name of the column containing junction sequences. Also used to determine sequence length for grouping.
v_call
character name of the column containing the V-segment allele calls.
j_call
character name of the column containing the J-segment allele calls.
clone
the output column name containing the clone ids.
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.
targeting_model
TargetingModel object. Only applicable if method="vj". See Details for description.
len_limit
IMGT_V object defining the regions and boundaries of the Ig sequences. If NULL, mutations are counted for entire sequence. Only applicable if method = "vj".
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 N’s to permit in the junction sequence before excluding the record from clonal assignment. Default is set to be zero. Set it as "NULL" for no action.
threshold
the supervising cut-off to enforce an upper-limit distance for clonal grouping. A numeric value between (0,1).
base_sim
required similarity cut-off for sequences in equal distances from each other.
iter_max
the maximum number of iterations allowed for kmean clustering step.
nstart
the number of random sets chosen for kmean clustering initialization.
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.

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.

Details

If method="novj", then clonal relationships are inferred using an adaptive threshold that indicates the level of similarity among junction sequences in a local neighborhood.

If method="vj", then clonal relationships are inferred not only on junction region homology, but also taking into account the mutation profiles in the V and J segments. Mutation counts are determined by comparing the input sequences (in the column specified by sequence) to the effective germline sequence (IUPAC representation of sequences in the column specified by germline).

While not mandatory, the influence of SHM hot-/cold-spot biases in the clonal inference process will be noted if a SHM targeting model is provided through the targeting_model argument. See TargetingModel for more technical details.

If the threshold argument is specified, then an upper limit for clonal grouping will be imposed to prevent sequences with dissimilarity above the threshold from grouping together. Any sequence with a distance greater than the threshold value from the other sequences, will be assigned to a singleton group.

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 and 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 were 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

# Subset example data
db <- subset(ExampleDb, sample_id == "-1h")

# Find clonal groups
results <- spectralClones(db, method="novj", germline="germline_alignment_d_mask")

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

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

2

See also

See plotCloneSummary for plotting summary results. See groupGenes for more details about grouping requirements.