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Apply Gate

Source: R/apply_gate.R
apply.gate.Rd

Applies a previously-defined scatter gate boundary to a set of flow cytometry expression data and returns only the events falling inside it. This is a lightweight, standalone counterpart to the gating step used internally by get.gated.flow.expression.data(), intended for interactive use and for testing other AutoSpectral functions against a gated subset of data without going through the full control-file/FCS-reading pipeline.

Usage

apply.gate(
  flow.data,
  gate.boundary,
  scatter.param = asp$default.scatter.parameter,
  asp = NULL,
  min.fraction = 0.01
)

Arguments

flow.data

A matrix or data frame of flow cytometry data (for example, unmixed or raw expression data) with named columns, including the two scatter parameters named in scatter.param.

gate.boundary

A gate boundary, as returned by define.gate.landmarks(), define.gate.density(), or do.gate() — a list containing at least numeric x and y components describing the polygon vertices.

scatter.param

Character vector of length 2 giving the names of the two scatter columns in flow.data to gate on. Default is asp$default.scatter.parameter.

asp

The AutoSpectral parameter list, prepared using get.autospectral.param(). Only used to supply the default for scatter.param; not required if scatter.param is supplied directly.

min.fraction

Numeric between 0 and 1, default 0.01. If the fraction of events retained by the gate falls below this value, a warning is issued (the function still returns the gated data). Set to 0 to disable this check.

Value

flow.data, subset to only those events falling inside gate.boundary.

See also