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GerminalCenter

Source: R/GerminalCenter.R
GerminalCenter.Rd

Models T follicular helper (Tfh) cell selection pressure on B cells within a germinal center reaction. Implements resource competition where antibodies compete for Tfh help, and only helped antibodies survive.

Details

The germinal center is where B cells undergo affinity maturation through iterative cycles of mutation and selection. Tfh cells act as quality-control selectors:

  • Each Tfh evaluates B cell (antibody) quality using a task-aware metric

  • B cells compete for Tfh help (resource competition)

  • Only helped B cells survive to the next round

  • Selection pressure controls the stringency of the process

Public fields

nTfh

Number of Tfh selectors (determines how many antibodies survive).

selectionPressure

Numeric [0,1]. 0 = no selection (all survive), 1 = only the very best survive.

rounds

Number of selection rounds per call.

Methods

Public methods

Method new()

Create a new GerminalCenter.

Usage

GerminalCenter$new(nTfh = 10, selectionPressure = 0.5, rounds = 1)

Arguments

nTfh

Integer. Number of Tfh helper cells. Each helps one B cell.

selectionPressure

Numeric [0,1]. Stringency of selection.

rounds

Integer. Number of competition rounds.

Method select()

Run germinal center selection on a repertoire.

Usage

GerminalCenter$select(
  repertoire,
  X,
  y = NULL,
  task = "clustering",
  affinityFunc = "gaussian",
  affinityParams = list(alpha = 1, c = 1, p = 2)
)

Arguments

repertoire

An ImmuneRepertoire object.

X

Numeric matrix of training data.

y

Target vector (factor or numeric) or NULL for clustering.

task

Character: "clustering", "classification", or "regression".

affinityFunc

Character. Affinity function for evaluation.

affinityParams

List. Parameters for affinity function.

Returns

Invisible self. Repertoire modified in place.

Method print()

Print summary.

Usage

GerminalCenter$print(...)

Arguments

...

Not used.

Method clone()

The objects of this class are cloneable with this method.

Usage

GerminalCenter$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

# Germinal center selection on Iris
data(iris)
X <- as.matrix(iris[, 1:4])
gc <- GerminalCenter$new(nTfh = 5, selectionPressure = 0.5)
rep <- ImmuneRepertoire$new(X[sample(150, 20), ])
gc$select(rep, X, iris$Species, "classification")
rep$size()  # fewer antibodies after selection
#> [1] 12