ClassSwitcher

Implements antibody isotype/class switching, allowing antibodies to change their matching breadth. Inspired by real B cell class switching from IgM (broad, pentameric) to IgG (specific, monomeric) to IgA (mucosal).

Details

In bHIVE, class switching modifies the effective affinity kernel width:

• IgM: Broad matching (large kernel width) – good for initial exploration and capturing general patterns

• IgG: Specific matching (small kernel width) – good for fine-grained discrimination after patterns are identified

• IgA: Boundary patrol (medium kernel width) – good for maintaining coverage at decision boundaries

Public fields

alpha_IgM

Kernel width for IgM mode (broad).

alpha_IgG

Kernel width for IgG mode (specific).

alpha_IgA

Kernel width for IgA mode (boundary).

Methods

Public methods

• ClassSwitcher$new()

• ClassSwitcher$switch_isotypes()

• ClassSwitcher$get_alpha()

• ClassSwitcher$print()

• ClassSwitcher$clone()

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Method new()

Create a new ClassSwitcher.

Usage

ClassSwitcher$new(alpha_IgM = 0.1, alpha_IgG = 5, alpha_IgA = 1)

Arguments

alpha_IgM

Numeric. Kernel width for broad matching.

alpha_IgG

Numeric. Kernel width for specific matching.

alpha_IgA

Numeric. Kernel width for boundary matching.

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Method switch_isotypes()

Determine appropriate isotype for each antibody based on its microenvironment zone.

Usage

ClassSwitcher$switch_isotypes(repertoire, zones)

Arguments

repertoire

An ImmuneRepertoire.

zones

Character vector from Microenvironment assessment.

Returns

Named numeric vector of alpha values per antibody.

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Method get_alpha()

Get alpha value for a given isotype.

Usage

ClassSwitcher$get_alpha(isotype)

Arguments

isotype

Character. "IgM", "IgG", or "IgA".

Returns

Numeric.

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Method print()

Print summary.

Usage

ClassSwitcher$print(...)

Arguments

...

Not used.

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Method clone()

The objects of this class are cloneable with this method.

Usage

ClassSwitcher$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

# Switch antibody isotypes based on microenvironment zones
A <- matrix(rnorm(50), nrow = 10, ncol = 5)
rep <- ImmuneRepertoire$new(A)
cs <- ClassSwitcher$new(alpha_IgM = 0.1, alpha_IgG = 5.0)
zones <- sample(c("stable", "explore", "boundary"), 10, replace = TRUE)
alphas <- cs$switch_isotypes(rep, zones)
table(rep$metadata$isotype)  # IgM, IgG, IgA distribution
#> 
#> IgA IgG IgM 
#>   1   3   6