makeGOGraph             package:GOstats             R Documentation

_C_o_n_s_t_r_u_c_t _a _G_O _G_r_a_p_h

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

     The directed acyclic graph (DAG) based on finding the most
     specific terms for the supplied Entrez Gene IDs is constructed and
     returned. The constructuion is per GO ontology (there are three,
     MF, BP and CC) and once the most specific terms have been
     identified then all less specific terms are found (these are the
     parents of the terms) and then their parents and so on, until the
     root is encountered.

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

     makeGOGraph(x, Ontology="MF", removeRoot = TRUE)

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

       x: A vector of Entrez Gene IDs. 

Ontology: Which of the GO ontologies to use. 

removeRoot: A logical value indicating whether the GO root node should
          be removed or not.

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

     For each supplied Entrez Gene identifier all the GO annotations
     (in the specified ontology) are found.

     The mappings are different for the different ontologies. Typically
     a GO indentifier is used only in one specific ontology.

     The resulting structure is stored in a graph using the 'graph'
     package, again from Bioconductor.

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

     An object that inherits from the 'graph' class. The particular
     implementation is not specified.

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

     R. Gentleman

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

     The Gene Ontology Consortium

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

     'oneGOGraph'

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

      gN <- c("71733","224019", "237928", "11308")
      gg1 <- makeGOGraph(gN, "BP")
      

