VDJLibrary

V(D)J gene library initialization for antibody populations. Instead of random sampling, antibodies are generated by combinatorial assembly of gene segments, mimicking the V(D)J recombination that generates antibody diversity in real immune systems.

Details

The feature space is decomposed into V, D, and J segments (subsets of dimensions). Each segment is discretized into "alleles" by clustering. New antibodies are generated by combinatorial sampling of one allele from each segment, producing structured coverage of the data manifold.

Methods:

• "pca": PCA components define gene segments

• "cluster": k-means within dimension groups creates alleles

• "random_partition": Random feature grouping

Public fields

nV

Number of V gene segments.

nD

Number of D gene segments.

nJ

Number of J gene segments.

method

Decomposition method.

library

The computed gene library (list of allele matrices).

Methods

Public methods

• VDJLibrary$new()

• VDJLibrary$build()

• VDJLibrary$generate()

• VDJLibrary$print()

• VDJLibrary$clone()

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Method new()

Create a new VDJLibrary.

Usage

VDJLibrary$new(nV = 10, nD = 5, nJ = 4, method = "pca")

Arguments

nV

Integer. Number of V gene alleles.

nD

Integer. Number of D gene alleles.

nJ

Integer. Number of J gene alleles.

method

Character. "pca", "cluster", or "random_partition".

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Method build()

Build the gene library from training data.

Usage

VDJLibrary$build(X)

Arguments

X

Numeric matrix (n x d).

Returns

Invisible self.

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Method generate()

Generate antibodies by combinatorial V(D)J assembly.

Usage

VDJLibrary$generate(nAntibodies, X)

Arguments

nAntibodies

Integer. Number of antibodies to generate.

X

Numeric matrix. Training data (used to build library if needed).

Returns

Numeric matrix (nAntibodies x d).

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Method print()

Print summary.

Usage

VDJLibrary$print(...)

Arguments

...

Not used.

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Method clone()

The objects of this class are cloneable with this method.

Usage

VDJLibrary$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

# Generate antibodies via V(D)J combinatorial assembly
data(iris)
X <- as.matrix(iris[, 1:4])
vdj <- VDJLibrary$new(nV = 5, nD = 3, nJ = 3, method = "pca")
A <- vdj$generate(20, X)
dim(A)  # 20 x 4
#> [1] 20  4
print(vdj)
#> <VDJLibrary> method='pca' V=5 D=3 J=3
#>   Combinatorial space: 45 antibodies