stam.net                package:stam                R Documentation

_G_e_n_e_r_a_t_e _a _C_l_a_s_s_i_f_i_e_r _G_r_a_p_h _f_o_r _S_t_A_M

_D_e_s_c_r_i_p_t_i_o_n:

     Generates a classifier graph for structured analysis of microarray
     data based on the Gene Ontology.

_U_s_a_g_e:

       stam.net(chip = "hgu95av2", root = "GO:0008150", probes = character(0))

_A_r_g_u_m_e_n_t_s:

    chip: A character string representing the microarray chip from
          which data has been generated. A meta data packages of the
          same name is used to obtain the annotation  data, namely for
          the Gene Ontology.

    root: The identifier of the GO node to be used as the root of the
          classifier  graph. Only successors of this node are
          considered to generate the graph.

  probes: The probe names in the order as they occur in the expression
          matrix.  Indeces according to this character array are used
          to index probes/probesets.

_D_e_t_a_i_l_s:

     stam.net crawls through the Gene Ontology starting with the root
     node specified. It  collects all successors of the root into a
     classifier graph according to the  parent-children relations
     defined in the Gene Ontology. Probesets of the microarray chip at
     hand are attributed to GO nodes according to the Bioconductor
     annotation  meta data package for the chip. 

     For any node i which has GO annotations AND successors an
     additional node i' is  introduced to the classifier graph. The new
     node is added as an additional child to i  and all probesets
     annotated to i are moved to i', such that only leaf nodes hold 
     probesets. Nodes which neither themselves nor any of their
     successors hold probesets  are discarded. stam.net also replaces
     inner nodes with only one child by their  successor.

_V_a_l_u_e:

     An object of class stamNet is returned. You may use the print
     method to obtain detailed information about the classifier graph.
     You may further investigate any element of the  'nodes' list using
     the print method.

_A_u_t_h_o_r(_s):

     Claudio Lottaz

_S_e_e _A_l_s_o:

     'stamNet-class', 'stam.writeHTML'

_E_x_a_m_p_l_e_s:

     ## Not run: 
     # load some data
     library(golubEsets)
     data(Golub_Merge)
     emat <- exprs(Golub_Merge)

     # determine classifier graph for chip "hu6800" on
     # biological processes, taking the positions of 
     # probesets in Golub's expression matrix into account
     net <- stam.net(chip="hu6800", root="GO:0003674", probes=rownames(emat))

     # have a look
     print(net)
     print(net@nodes[[16]])
     print(net@nodes$"GO:0007638")
     ## End(Not run)

