qtclust {flexclust} | R Documentation |
Perform stochastic QT clustering on a data matrix.
qtclust(x, radius, family = kccaFamily("kmeans"), control = NULL, save.data=FALSE, kcca=FALSE)
x |
A numeric matrix of data, or an object that can be coerced to such a matrix (such as a numeric vector or a data frame with all numeric columns). |
radius |
Maximum radius of clusters. |
family |
Object of class |
control |
An object of class |
.
save.data |
Save a copy of |
kcca |
Run |
This function implements a generalization of the QT clustering algorithm by
Heyer et al. (1999), see Scharl and Leisch (2006). The only difference
is that in each iteration not
all possible cluster start points are considered, but only a random
sample of size control@ntry
. In most cases the resulting
solutions are almost
the same at a considerable speed increase, in some cases even better
solutions are obtained than with the original algorithm. If
control@ntry
is
set to the size of the data set, the original algorithm as proposed by
Heyer et al. (1999) is obtained.
Function qtclust
by default returns objects of class
"kccasimple"
. If argument kcca
is TRUE
, function
kcca()
is run afterwards (initialized on the QT cluster
solution). Data points
not clustered by the QT cluster algorithm are omitted from the
kcca()
iterations, but filled back into the return
object. All plot methods defined for objects of class "kcca"
can be used.
Friedrich Leisch
Heyer, L. J., Kruglyak, S., Yooseph, S. (1999). Exploring expression data: Identification and analysis of coexpressed genes. Genome Research 9, 1106–1115.
Theresa Scharl and Friedrich Leisch. The stochastic QT-clust algorithm: evaluation of stability and variance on time-course microarray data. In Alfredo Rizzi and Maurizio Vichi, editors, Compstat 2006 – Proceedings in Computational Statistics, pages 1015-1022. Physica Verlag, Heidelberg, Germany, 2006.
x <- matrix(10*runif(1000), ncol=2) ## maximum distrance of point to cluster center is 3 cl1 <- qtclust(x, radius=3) ## maximum distrance of point to cluster center is 1 ## -> more clusters, longer runtime cl2 <- qtclust(x, radius=1) opar <- par(c("mfrow","mar")) par(mfrow=c(2,1), mar=c(2.1,2.1,1,1)) plot(x, col=predict(cl1), xlab="", ylab="") plot(x, col=predict(cl2), xlab="", ylab="") par(opar)