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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.

last_survivors

Integer vector of survivor indices (relative to the input repertoire) from the most recent call to select().

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

Factor target vector or NULL for clustering.

task

Character: "clustering" or "classification".

affinityFunc

Character. Affinity function for evaluation.

affinityParams

List. Parameters for affinity function.

Returns

Integer vector of survivor indices relative to the input repertoire (composed across all selection rounds). Also stored on self$last_survivors for inspection. Repertoire is 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