maigesPack (version 1.30.0)

somMde: Function to do SOM cluster analysis

Description

This is a function to do SOM (Self Organising Maps) clustering analysis for objects of classes maigesDEcluster.

Usage

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, ...)

Arguments

data

object of class maigesDEcluster.

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.

idxTest

numerical index of the test to be used to sort the genes when clustering objects of class maigesDEcluster.

adjP

string specifying the method of p-value adjustment. May be 'none', 'Bonferroni', 'Holm', 'Hochberg', 'SidakSS', 'SidakSD', 'BH', 'BY'.

nDEgenes

number of DE genes to be selected. If a real number in (0,1) all genes with p.value <= nDEgenes will be used. If an integer, the nDEgenes genes with smaller p-values will be used.

...

additional parameters for som function.

Value

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

Details

This function implements the SOM clustering method for objects resulted from differential expression analysis. The method uses the function som from package som. For the adjustment of p-values in the selection of genes differentially expressed, we use the function mt.rawp2adjp from package multtest.

See Also

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

Examples

## 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")