safedag                 package:safe                 R Documentation

_S_A_F_E _r_e_s_u_l_t_s _d_i_s_p_l_a_y_e_d _i_n _G_e_n_e _O_n_t_o_l_o_g_y

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

     SAFE results are displayed on the directed acyclic graph for one
     of the ontologies under investigation.  Category-wide significance
     displayed by node color.

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

  object: Object of class 'SAFE' 

ontology: Gene Ontology of interest. Character strings of "GO.CC",
          "GO.BP", and "GO.MF" accepted.

     top: Optional character string giving the node name from which to
          draw a subgraph of the tree

    file: Optional filename for a post-script of the graph 

color.cutoffs: Numeric vector of length 3 for the cutoffs for coloring
          significant nodes. Nodes with unadjusted p-values less than
          'color.cutoff[3]' are drawn in blue; less than
          'color.cutoff[2]' are drawn in green; less than
          'color.cutoff[1]' are drawn in red.

  filter: Optional integer (1,2,3) to only include branches that
          contain at least one node as significant as the respective
          color.cutoff. 

max.GOnames: Maximum size of DAG to include category names as labels.

_D_e_t_a_i_l_s:

     DAG-plots are suggested as a means for visualizing the extent of
     differential expression in Gene Ontology categories. The
     relatedness of significant categories suggests whether similar or
     disparate biological findings are identified.

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

     William T. Barry: bill.barry@duke.edu

_R_e_f_e_r_e_n_c_e_s:

     W. T. Barry, A. B. Nobel and F.A. Wright, 2005, _Significance
     Analysis of functional categories in gene expression studies: a
     structured permutation approach_, _Bioinformatics_ {\bf 21}(9)
     1943-1949. 

     See also the vignette included with this package.

_S_e_e _A_l_s_o:

     {'safe'.}

