somM {maigesPack} | R Documentation |
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
.
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, ...)
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. |
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.
This function display the heatmaps and return invisibly an object
of class som
resulted from the function som
.
Gustavo H. Esteves <gesteves@vision.ime.usp.br>
som
from package som.
kmeansM
and hierM
for displaying k-means and
hierarchical clusters, respectively.
## 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")