somM: Function to do SOM cluster analysis

In maigesPack: Functions to handle cDNA microarray data, including several methods of data analysis

Description

This is a function to do SOM (Self Organising Maps) clustering analysis for objects of classes maiges, maigesRaw and maigesANOVA. Use the function somMde for objects of class maigesDEcluster.

Usage

somM(data, group=c("C", "R")[1], distance="correlation",
     method="complete", sampleT=NULL, doHier=FALSE, sLabelID="SAMPLE",
     gLabelID="GeneName", rmGenes=NULL, rmSamples=NULL, rmBad=TRUE,
     geneGrp=NULL, path=NULL, ...)

Arguments

data	object of class maigesRaw, maiges, or maigesANOVA.
group	character string giving the type of grouping: by rows 'R' or columns 'C' (default).
distance	char string giving the type of distance to use. Only two options are available here: 'euclidean' and 'correlation' (default).
method	char string specifying the linkage method for the hierarchical cluster. Possible values are 'ward', 'single', 'complete' (default), 'average', 'mcquitty', 'median' or 'centroid'
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.
doHier	logical indicating if you want to do the hierarchical branch in the opposite dimension of clustering. Defaults to FALSE.
sLabelID	character string specifying the sample label ID to be used to label the samples.
gLabelID	character string specifying the gene label ID to be used to label the genes.
rmGenes	char list specifying genes to be removed.
rmSamples	char list specifying samples to be removed.
rmBad	logical indicating to remove or not bad spots (slot BadSpots in objects of class maiges, maigesRaw or maigesANOVA).
geneGrp	numerical or character specifying the gene group to be clustered. This is given by the columns of the slot GeneGrps in objects of classes maiges, maigesRaw and maigesANOVA.
path	numerical or character specifying the gene network to be clustered. This is given by the items of the slot Paths in objects of classes maiges, maigesRaw and maigesANOVA.
...	additional parameters for som function.

Details

This function implements the SOM clustering method for objects of microarray data defined in this package. The method uses the function som from package som.

Value

This function display the heatmaps and return invisibly an object of class som resulted from the function som.

Author(s)

Gustavo H. Esteves <[e-mail]>

See Also

som from package som. kmeansM and hierM for displaying k-means and hierarchical clusters, respectively.

Examples

## Loading the dataset
data(gastro)

## Doing a SOM cluster with 2 groups using all genes, for maigesRaw class
somM(gastro.raw, rmGenes=c("BLANK","DAP","LYS","PHE", "Q_GENE","THR","TRP"),
     sLabelID="Sample", gLabelID="Name", xdim=2, ydim=1, topol="rect")

## Doing a SOM cluster with 3 groups using all genes, for maigesNorm class
somM(gastro.norm, rmGenes=c("BLANK","DAP","LYS","PHE", "Q_GENE","THR","TRP"),
     sLabelID="Sample", gLabelID="Name", xdim=3, ydim=1, topol="rect")

## Another example with 4 groups
somM(gastro.norm, rmGenes=c("BLANK","DAP","LYS","PHE", "Q_GENE","THR","TRP"),
     sLabelID="Sample", gLabelID="Name", xdim=2, ydim=2, topol="rect")

## If you want to use euclidean distance to group genes (or spots), with
## 3 groups
somM(gastro.summ, rmGenes=c("BLANK","DAP","LYS","PHE", "Q_GENE","THR","TRP"),
     sLabelID="Sample", gLabelID="Name", group="R",
     distance="euclidean", xdim=3, ydim=1, topol="rect")

maigesPack documentation built on Nov. 8, 2020, 6:23 p.m.