somM               package:maigesPack               R Documentation

_F_u_n_c_t_i_o_n _t_o _d_o _S_O_M _c_l_u_s_t_e_r _a_n_a_l_y_s_i_s

_D_e_s_c_r_i_p_t_i_o_n:

     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'.

_U_s_a_g_e:

     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, ...)

_A_r_g_u_m_e_n_t_s:

    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.

_D_e_t_a_i_l_s:

     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_.

_V_a_l_u_e:

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

_A_u_t_h_o_r(_s):

     Gustavo H. Esteves <gesteves@vision.ime.usp.br>

_S_e_e _A_l_s_o:

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

_E_x_a_m_p_l_e_s:

     ## 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")

