distToNearest

distToNearest - Distance to nearest neighbor

Description¶

Calculate the non-zero distance from each sequence to its nearest neighbor within partitions based on shared V gene, J gene, and junction length.

Usage¶

distToNearest(
db,
sequenceColumn = "junction",
vCallColumn = "v_call",
jCallColumn = "j_call",
model = c("ham", "aa", "hh_s1f", "hh_s5f", "mk_rs1nf", "mk_rs5nf", "m1n_compat",
"hs1f_compat"),
normalize = c("len", "none"),
symmetry = c("avg", "min"),
first = TRUE,
VJthenLen = TRUE,
nproc = 1,
fields = NULL,
cross = NULL,
mst = FALSE,
subsample = NULL,
progress = FALSE,
cellIdColumn = NULL,
locusColumn = "locus",
locusValues = c("IGH"),
onlyHeavy = TRUE,
keepVJLgroup = TRUE
)

Arguments¶

db: data.frame containing sequence data.
sequenceColumn: name of the column containing the junction for grouping and for calculating nearest neighbor distances. Note that while both heavy/long and light/short chain junctions may be used for V-J-length grouping, only the heavy/long chain (IGH, TRB, TRD) junction is used to calculate distances.
vCallColumn: name of the column containing the V-segment allele calls.
jCallColumn: name of the column containing the J-segment allele calls.
model: underlying SHM model, which must be one of c("ham", "aa", "hh_s1f", "hh_s5f", "mk_rs1nf", "hs1f_compat", "m1n_compat"). See Details for further information.
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.
symmetry: if model is hs5f, distance between seq1 and seq2 is either the average (avg) of seq1->seq2 and seq2->seq1 or the minimum (min).
first: 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.
VJthenLen: logical value specifying whether to perform partitioning as a 2-stage process. If TRUE, partitions are made first based on V and J gene, and then further split based on junction lengths corresponding to sequenceColumn. If FALSE, perform partition as a 1-stage process during which V gene, J gene, and junction length are used to create partitions simultaneously. Defaults to TRUE.
nproc: number of cores to distribute the function over.
fields: additional fields to use for grouping.
cross: character vector of column names to use for grouping to calculate distances across groups. Meaning the columns that define self versus others.
mst: if TRUE, return comma-separated branch lengths from minimum spanning tree.
subsample: number of sequences to subsample for speeding up pairwise-distance-matrix calculation. Subsampling is performed without replacement in each V-J-length group of heavy chain sequences. If subsample is larger than the unique number of heavy chain sequences in each VJL group, then the subsampling process is ignored for that group. For each heavy chain sequence in db, the reported dist_nearest is the distance to the closest heavy chain sequence in the subsampled set for the V-J-length group. If NULL no subsampling is performed.
progress: if TRUE print a progress bar.
cellIdColumn: name of the character column containing cell identifiers or barcodes. If specified, grouping will be performed in single-cell mode with the behavior governed by the locusColumn and onlyHeavy arguments. If set to NULL then the bulk sequencing data is assumed.
locusColumn: name of the column containing locus information. Valid loci values are “IGH”, “IGI”, “IGK”, “IGL”, “TRA”, “TRB”, “TRD”, and “TRG”.
locusValues: Loci values to focus the analysis on.
onlyHeavy: This is deprecated. Only IGH (BCR) or TRB/TRD (TCR) sequences will be used for grouping. Only applicable to single-cell data. Ignored if cellIdColumn=NULL. See groupGenes for further details.
keepVJLgroup: logical value specifying whether to keep in the output the the column column indicating grouping based on V-J-length combinations. Only applicable for 1-stage partitioning (i.e. VJthenLen=FALSE). Also see groupGenes.

Value¶

Returns a modified db data.frame with nearest neighbor distances between heavy chain sequences in the dist_nearest column if cross=NULL. If cross was specified, distances will be added as the cross_dist_nearest column.

Note that distances between light/short (IGK, IGL, TRA, TRG) chain sequences are not calculated, even if light/short chains were used for V-J-length grouping via onlyHeavy=FALSE. Light/short chain sequences, if any, will have NA in the dist_nearest output column.

Note that the output vCallColumn and jCallColumn columns will be converted to type character if they were type factor in the input db.

Details¶

The distance to nearest neighbor can be used to estimate a threshold for assigning Ig sequences to clonal groups. A histogram of the resulting vector is often bimodal, with the ideal threshold being a value that separates the two modes.

Refer to the details section for a more thorough description of the implementation.

There are two modes of operation for distToNearest: single-cell (all sequences are single-cell data), non-single-cell (all sequences are bulk sequencing data). Mixed data, where both single-cell and non-single-cell sequences are present in the data, is considered a case under the single-single cell mode .

To invoke single-cell mode the cellIdColumn argument must be specified and locusColumn must be correct. Otherwise, distToNearest will be run with bulk sequencing assumptions, using all input sequences regardless of the values in the locusColumn column.

Under single-cell mode, only heavy/long chain (IGH, TRB, TRD) sequences will be used for calculating nearest neighbor distances regardless of locusValue values in the locusColumn field (if present). Under non-single-cell mode, all input sequences with locusValue value(s) in the locusColumn field will be used for calculating nearest neighbor distances.

Values in the locusColumn must be one of c("IGH", "IGI", "IGK", "IGL") for BCR or c("TRA", "TRB", "TRD", "TRG") for TCR sequences. Otherwise, the function returns an error message and stops.

For single-cell mode, the input format is the same as that for groupGenes. Namely, each row represents a sequence/chain. Sequences/chains from the same cell are linked by a cell ID in the cellIdColumn field. Grouping will be done by using IGH (BCR) or TRB/TRD (TCR) sequences only. The argument that allowed to include light chains, onlyHeavy, is deprecated.

Note, distToNearest required that each cell (each unique value in cellIdColumn) correspond to only a single IGH (BCR) or TRB/TRD (TCR) sequence.

The following distance measures are accepted by the model parameter.

"ham": Single nucleotide Hamming distance matrix from getDNAMatrix with gaps assigned zero distance.
"aa": Single amino acid Hamming distance matrix from getAAMatrix.
"hh_s1f": Human single nucleotide distance matrix derived from HH_S1F with calcTargetingDistance.
"hh_s5f": Human 5-mer nucleotide context distance matrix derived from HH_S5F with calcTargetingDistance.
"mk_rs1nf": Mouse single nucleotide distance matrix derived from MK_RS1NF with calcTargetingDistance.
"mk_rs5nf": Mouse 5-mer nucleotide context distance matrix derived from MK_RS5NF with calcTargetingDistance.
"hs1f_compat": Backwards compatible human single nucleotide distance matrix used in SHazaM v0.1.4 and Change-O v0.3.3.
"m1n_compat": Backwards compatibility mouse single nucleotide distance matrix used in SHazaM v0.1.4 and Change-O v0.3.3.

Note on NAs: if, for a given combination of V gene, J gene, and junction length, there is only 1 heavy chain sequence (as defined by sequenceColumn), NA is returned instead of a distance (since it has no heavy/long chain neighbor). If for a given combination there are multiple heavy/long chain sequences but only 1 unique one, (in which case every heavy/long chain sequence in this group is the de facto nearest neighbor to each other, thus giving rise to distances of 0), NAs are returned instead of zero-distances.

Note on subsample: Subsampling is performed independently in each V-J-length group for heavy/long chain sequences. If subsample is larger than number of heavy/long chain sequences in the group, it is ignored. In other words, subsampling is performed only on groups in which the number of heavy/long chain sequences is equal to or greater than subsample. dist_nearest has values calculated using all heavy chain sequences in the group for groups with fewer than subsample heavy/long chain sequences, and values calculated using a subset of heavy/long chain sequences for the larger groups. To select a value of subsample, it can be useful to explore the group sizes in db (and the number of heavy/long chain sequences in those groups).

References¶

Smith DS, et al. Di- and trinucleotide target preferences of somatic mutagenesis in normal and autoreactive B cells. J Immunol. 1996 156:2642-52.
Glanville J, Kuo TC, von Budingen H-C, et al. Naive antibody gene-segment frequencies are heritable and unaltered by chronic lymphocyte ablation. Proc Natl Acad Sci USA. 2011 108(50):20066-71.
Yaari G, et al. Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data. Front Immunol. 2013 4:358.

Examples¶

# Subset example data to one sample as a demo
data(ExampleDb, package="alakazam")
db <- subset(ExampleDb, sample_id == "-1h")

# Use genotyped V assignments, Hamming distance, and normalize by junction length
# First partition based on V and J assignments, then by junction length
# Take into consideration ambiguous V and J annotations
dist <- distToNearest(db, sequenceColumn="junction", 
vCallColumn="v_call_genotyped", jCallColumn="j_call",
model="ham", first=FALSE, VJthenLen=TRUE, normalize="len")

Running in non-single-cell mode.


# Plot histogram of non-NA distances
p1 <- ggplot(data=subset(dist, !is.na(dist_nearest))) + 
theme_bw() + 
ggtitle("Distance to nearest: Hamming") + 
xlab("distance") +
geom_histogram(aes(x=dist_nearest), binwidth=0.025, 
fill="steelblue", color="white")
plot(p1)