mkPrior-methods: Generate FlowClust prior Specifications

Description

Generate FlowClust Prior Specification from Existing gates on multiple samples

Arguments

Methods

signature(gate = "missing", data = "flowSet", nu0 = "ANY", Omega0 = "missing"): Generate a prior from a flowSet. All the dimensions will be used. Presumably each flowFrame in the flowSet contains a subset of the data that is of interest. Hyperparameters are estimated from the data.
signature(gate = "missing", data = "flowFrame", nu0 = "missing", Omega0 = "missing"): Generate a prior from a flowFrame only. All the dimensions are used. Hyperparameters are estimated from the data.
signature(gate = "list", data = "GatingSet", nu0 = "ANY", Omega0 = "missing"): Generate a prior based on a list of gates and a GatingSet object. nu0 and Omega0 are not specified but estimated from the data. Generally should not be called by the user but via the mkPriorTree method.
signature(gate = "list", data = "flowSet", nu0 = "ANY", Omega0 = "missing"): Generate a prior specification from a list of gates and a flowSet of samples. Each gate will be applied to each sample in the flowSet and a prior derived from the resulting sample means and covariances.
signature(gate = "polygonGate", data = "flowFrame", nu0 = "missing", Omega0 = "missing"): Should not be called by the user. Returns the mean and covariance of data in a polygonGate, as well as the number of events, used by other methods to construct a complete prior specification.
signature(gate = "polygonGate", data = "flowFrame", nu0 = "numeric", Omega0 = "matrix"): Generates a prior specification using the data in a polygonGate. Hyperparameters nu0, and Omega0 are specified by the user, the rest are estimated from the data.
signature(gate = "rectangleGate", data = "flowFrame", nu0 = "missing", Omega0 = "missing"): Should not be called by the user. Returns the mean and covariance of data in a rectangleGate, as well as the number of events, used by other methods to construct a complete prior specification.
signature(gate = "rectangleGate", data = "flowFrame", nu0 = "numeric", Omega0 = "matrix"): Generates a prior specification using the data in a rectangleGate. Hyperparameters nu0, and Omega0 are specified by the user, the rest are estimated from the data.