som {GeneSOM} | R Documentation |
Produces an object of class "som" which is a Self-Organizing Map fit of the data.
som(data, xdim, ydim, init="linear", alpha=NULL, alphaType="inverse", neigh="gaussian", topol="rect", radius=NULL, rlen=NULL)
data |
a data frame or matrix of input data. |
xdim |
an integer specifying the x-dimension of the map. |
ydim |
an integer specifying the y-dimension of the map. |
init |
a character string specifying the initializing method. The following
are permitted:
"sample" uses a radom sample from the data;
"random" uses random draws from N(0,1);
"linear" uses the linear grids upon the first two principle
components directin.
|
alpha |
a vector of initial learning rate parameter for the two training phases. Decreases linearly to zero during training. |
alphaType |
a character string specifying learning rate funciton type. Possible
choices are linear function ("linear" ) and inverse-time type
function ("inverse" ).
|
neigh |
a character string specifying the neighborhood function type. The
following are permitted:
"bubble"
"gaussian"
|
topol |
a character string specifying the topology type when measuring
distance in the map. The following are permitted:
"hexa"
"rect"
|
radius |
a vector of initial radius of the training area in som-algorithm for the two training phases. Decreases linearly to one during training. |
rlen |
a vector of running length (number of steps) in the two training phases. |
An object of class "som"
representing the fit.
Jun Yan <jyan@stat.wisc.edu>
data(yeast) yeast <- yeast[, -c(1, 11)] yeast.f <- filtering(yeast) yeast.f.n <- normalize(yeast.f) foo <- som(yeast.f.n, xdim=5, ydim=6) foo <- som(yeast.f.n, xdim=5, ydim=6, topol="hexa", neigh="gaussian")