\HeaderA{somMde}{Function to do SOM cluster analysis}{somMde}
\keyword{hplot}{somMde}
\begin{Description}\relax
This is a function to do SOM (Self Organising Maps) clustering
analysis for objects of classes \code{\LinkA{maigesDEcluster}{maigesDEcluster}}.
\end{Description}
\begin{Usage}
\begin{verbatim}
somMde(data, group=c("C", "R")[1], distance="correlation",
       method="complete", sampleT=NULL, doHier=FALSE, sLabelID="SAMPLE",
       gLabelID="GeneName", idxTest=1, adjP="none", nDEgenes=0.05, ...)

\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{data}] object of class \code{\LinkA{maigesDEcluster}{maigesDEcluster}}.
\item[\code{group}] character string giving the type of grouping: by rows
'R' or columns 'C' (default).
\item[\code{distance}] char string giving the type of distance to use. Only two
options are available here: 'euclidean' and 'correlation' (default).
\item[\code{method}] char string specifying the linkage method for the
hierarchical cluster. Possible values are 'ward', 'single',
'complete' (default), 'average', 'mcquitty', 'median' or 'centroid'
\item[\code{sampleT}] list with 2 vectors. The first one specify the first
letter of different sample types to be coloured by distinct colours,
that are given in the second vector. If NULL (default) no colour is used.
\item[\code{doHier}] logical indicating if you want to do the hierarchical
branch in the opposite dimension of clustering. Defaults to FALSE.
\item[\code{sLabelID}] character string specifying the sample label ID to be
used to label the samples.
\item[\code{gLabelID}] character string specifying the gene label ID to be
used to label the genes.
\item[\code{idxTest}] numerical index of the test to be used to sort the
genes when clustering objects of class \code{\LinkA{maigesDEcluster}{maigesDEcluster}}.
\item[\code{adjP}] string specifying the method of p-value adjustment. May be
'none', 'Bonferroni', 'Holm', 'Hochberg', 'SidakSS', 'SidakSD',
'BH', 'BY'.
\item[\code{nDEgenes}] number of DE genes to be selected. If a real number
in (0,1) all genes with p.value <= \code{nDEgenes} will be
used. If an integer, the \code{nDEgenes} genes with smaller
p-values will be used.
\item[\code{...}] additional parameters for \code{\LinkA{som}{som}} function.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function implements the SOM clustering method for
objects resulted from differential expression analysis. The method uses
the function \code{\LinkA{som}{som}} from package \emph{som}. For
the adjustment of p-values in the selection of genes differentially
expressed, we use the function \code{\LinkA{mt.rawp2adjp}{mt.rawp2adjp}}
from package \emph{multtest}.
\end{Details}
\begin{Value}
This function display the heatmaps and return invisibly an object
of class \code{som} resulted from the function \code{\LinkA{som}{som}}.
\end{Value}
\begin{Author}\relax
Gustavo H. Esteves <\email{gesteves@vision.ime.usp.br}>
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{som}{som}} from package \emph{som}.
\code{\LinkA{kmeansM}{kmeansM}} and \code{\LinkA{hierM}{hierM}} for displaying k-means and
hierarchical clusters, respectively.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Loading the dataset
data(gastro)

## Doing bootstrap from t statistic test fot 'Type' sample label, k=1000
## specifies one thousand bootstraps
gastro.ttest = deGenes2by2Ttest(gastro.summ, sLabelID="Type")

## SOM cluster with 2 groups adjusting p-values by FDR, and showing all genes
## with p-value < 0.05
somMde(gastro.ttest, sLabelID="Type", adjP="BH", nDEgenes=0.05,
       xdim=2, ydim=1, topol="rect")

## SOM cluster with 4 groups adjusting p-values by FDR, and showing all genes
## with p-value < 0.05
somMde(gastro.ttest, sLabelID="Type", adjP="BH", nDEgenes=0.05,
       xdim=2, ydim=2, topol="rect")
\end{ExampleCode}
\end{Examples}

