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 identifiers 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, what="MF", lib="hgu95av2", removeRoot = TRUE)

_A_r_g_u_m_e_n_t_s:

       x: A vector of identifiers. 

    what: Which of the GO ontologies to use. 

     lib: The name of a meta-data package to use for mapping the
          identifiers to GO identifiers. 

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

_D_e_t_a_i_l_s:

     The mapping of manufacturers identifiers (e.g. Affymetrix) to GO
     identifiers is done on the basis of an initial mapping to
     LocusLink identifiers. For many data sources these are available
     from the Bioconductor Project (<URL: www.bioconductor.org>).

     Once that mapping has occurred we obtain from the meta-data
     package the mapping to the most specific terms (again these have
     been precomputed) and using those together with the GO package
     (again from Bioconductor) mapping to all parents down to the root
     node is performed.

     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("38940_at","2073_s_at", "35580_at",  "34701_at")
      gg1 <- makeGOGraph(gN, "BP", "hgu95av2")
      

