categoryToEntrezBuilder       package:PCpheno       R Documentation

_R_e_t_u_r_n _a _l_i_s_t _m_a_p_p_i_n_g _m_u_l_t_i-_p_r_o_t_e_i_n _c_o_m_p_l_e_x_e_s _I_D_s _t_o _Y_E_A_S_T _i_d_s

_D_e_s_c_r_i_p_t_i_o_n:

     Return a list mapping  multi-protein complexes (category) IDs to
     the YEAST ids annotated at the category id.

_U_s_a_g_e:

     ## S4 method for signature 'CoHyperGParams':
     categoryToEntrezBuilder(p)

_A_r_g_u_m_e_n_t_s:

       p: A subclass of 'HyperGParams-class'

_D_e_t_a_i_l_s:

     End users *should not* call this directly.  This method gets
     called from 'hyperGTest'.  To add support for a new category, a
     new method for this generic must be defined.  Its signature should
     match a subclass of 'HyperGParams-class' appropriate for the new
     category.

_V_a_l_u_e:

     A list mapping category IDs to YEAST identifiers.

_A_u_t_h_o_r(_s):

     S. Falcon and N. LeMeur

_S_e_e _A_l_s_o:

     'hyperGTest' 'CoHyperGParams-class'

_E_x_a_m_p_l_e_s:

     data(ScISIC)
     data(essglist)
     essential <- names(essglist)

     params <- new("CoHyperGParams",
                   geneIds=essential, 
                   universeGeneIds=rownames(ScISIC),
                   annotation="org.Sc.sgd.db",
                   categoryName="ScISIC",
                   pvalueCutoff=0.01,
                   testDirection="over")

     categoryToEntrezBuilder(params)[1:2]

