hgParams              package:ppiStats              R Documentation

_A _w_r_a_p_p_e_r _f_u_n_c_t_i_o_n _t_o _b_u_i_l_d _a _p_a_r_a_m_e_t_e_r _c_l_a_s_s _f_o_r _t_h_e 
_i_n_p_u_t _o_f _t_h_e _H_y_p_e_r_G_T_e_s_t.

_D_e_s_c_r_i_p_t_i_o_n:

     This function takes a gene set and conducts test for either over
     or under representation of some category using the Hypergeometric
     distribution.

     The two differences when building the parameter classes are that a
     conditional test can be performed on the GO dag but not on PFAM
     categories and an ontology can be assigned to GO but not to PFAM.

_U_s_a_g_e:

     ppiBuildParams4GO(geneSet, universe, direction="over", annot="org.Sc.sgd",
                                ontology = "CC", cond=TRUE, pThresh = 0.01)
     ppiBuildParams4PFAM(geneSet, universe, annot ="org.Sc.sgd",
                                   direction = "over", pThresh=0.01)

_A_r_g_u_m_e_n_t_s:

 geneSet: A character vector of genes given by the gene locus name.

universe: The set of genes by which the geneSet is tested against  for
          over/under representation. The genes are also given  by the
          gene locus names.

direction: A character. This parameter can be either set to over or
          under when testing for GO categories.

   annot: A character. The annotation package used.

ontology: A character: either CC, MF, or BP to describe the GO
          ontology.

    cond: A logical. To test within the CO dag, a conditional
          hypergeometric test can be conducted.

 pThresh: A numeric. A p-value threshold by which the null hypothesis
          is rejected.

_V_a_l_u_e:

     A object of class hyperGParams.

_A_u_t_h_o_r(_s):

     T Chiang

