Usage
HierarchicalSparseCluster.wrapper(file, method=c("average", "complete", "single", "centroid"),
wbound=NULL, silent=FALSE, cluster.features=FALSE,
method.features=c("average", "complete",
"single","centroid"),output.cluster.files=TRUE,outputfile.prefix=NULL,maxnumgenes=5000,standardize.arrays=TRUE)
Arguments
file
A GCT filename in the working directory containing the
data to be clustered.
method
The type of linkage to use in the hierarchical
clustering - "single", "complete", "average", or "centroid".
wbound
The L1 bound on w to use; this is the tuning parameter
for sparse hierarchical clustering. If NULL, then it will be
chosen via HierarchicalSparseCluster.permute.
silent
Print out progress?
cluster.features
Is a clustering for the features with non-zero
weights also desired? Default is FALSE.
method.features
If cluster.features is TRUE, then the type of
linkage used to cluster the features with non-zero weights: one of
"single", "complete", "average", or "centroid".
output.cluster.files
Should files containing the clustering be output? Default is
TRUE.
outputfile.prefix
The prefix for the output files. If NULL,
then the prefix of the input file is used.
maxnumgenes
Limit the analysis to some number of genes with highest marginal
variance, for computational reasons. This is recommended when the number of genes is very
large. If NULL, then all genes are used.
standardize.arrays
Should the arrays first be standardized?
Default is TRUE.