| posterior {flowClust} | R Documentation |
Various functions are available to retrieve the posterior probabilities of clustering memberships z (posterior), the “weights” u (importance), the uncertainty (uncertainty), and the estimates of the cluster means and proportions (getEstimates) resulted from the clustering (filtering) operation.
posterior(object, assign=FALSE) importance(object, assign=FALSE) uncertainty(object) getEstimates(object)
object |
Object returned from flowClust or filter. |
assign |
A logical value. If TRUE, only the quantity (z for posterior or u for importance) associated with the cluster to which an observation is assigned will be returned. Default is FALSE, meaning that the quantities associated with all the clusters will be returned. |
These functions are written to retrieve various slots contained in the object returned from the clustering operation. posterior and importance provide a means to conveniently retrieve information stored in object@z and object@u respectively. uncertainty is to retrieve object@uncertainty, and getEstimates is to retrieve information stored in object@mu (transformed back to the original scale) and object@w.
Denote by K the number of clusters, N the number of observations, and P the number of variables. For posterior and importance, a matrix of size N x K is returned if assign=FALSE (default). Otherwise, a vector of size N is outputted. uncertainty always outputs a vector of size N. getEstimates returns a list with two names elements, locations and proportions. locations is a matrix of size K x P and contains the estimates of the K mean vectors transformed back to the original scale (i.e., rbox(object@mu, object@lambda)). proportions is a vector of size P and contains the estimates of the K cluster proportions.
Raphael Gottardo <raph@stat.ubc.ca>, Kenneth Lo <c.lo@stat.ubc.ca>
Lo, K., Brinkman, R. R. and Gottardo, R. (2008) Automated Gating of Flow Cytometry Data via Robust Model-based Clustering. Cytometry A 73, 321-332.
res <- flowClust(iris[,1:4], K=3) posterior(res) posterior(res, assign=TRUE) importance(res) importance(res, assign=TRUE) uncertainty(res) getEstimates(res)