prepareAxis            package:goCluster            R Documentation

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_r_e_g_i_o_n_s _w_i_t_h _m_i_n_i_m_a_l _p-_v_a_l_u_e

_D_e_s_c_r_i_p_t_i_o_n:

     The function expects a tree representing clusters from a
     hierarchical clustering as input. Each cluster represented my
     contain only one selected annotation term per annotation. This is
     usually achieved by feeding the output of the 'minimizeSelection'
     output to this function as input. 'prepareAxis' will merge all
     overlapping clusters in the tree to the non-overlapping clusters
     with annotation terms of minimal p-values. This forms an axis
     along the genes originally used for clustering. When ordered
     according to the tree of the hierarchical clustering the vector
     can easily be used for display purposes.

_U_s_a_g_e:

     prepareAxis(minSelection, Clusters, annotations)

_A_r_g_u_m_e_n_t_s:

minSelection: The tree of representing the clusters of the hierarchical
          tree. Each cluster may only contain zero or one selected
          annotation terms per annotation.

Clusters: A tree of the same structure as given for 'minSelection' but
          each node identifies the genes included in that cluster. 

annotations: The number of annotations represented by the tree. 

_V_a_l_u_e:

     A list with a length that corresponds to the number of annotations
     present in the original tree. Each list item contains a vector
     that matches the list of genes. For each gene the annotation term
     with minimal p-values (if any) is given.

_A_u_t_h_o_r(_s):

     Gunnar Wrobel, <URL: http://www.gunnarwrobel.de>.

_E_x_a_m_p_l_e_s:

