modelSLGI                package:SLGI                R Documentation

_P_e_r_m_u_t_a_t_i_o_n _m_o_d_e_l _f_o_r _a_s_s_e_s_s_i_n_g _s_y_n_t_h_e_t_i_c _g_e_n_e_t_i_c _i_n_t_e_r_a_c_t_i_o_n_s _i_n
_c_e_l_l_u_l_a_r _o_r_g_a_n_i_z_a_t_i_o_n_a_l _u_n_i_t_s.

_D_e_s_c_r_i_p_t_i_o_n:

     Permutation model for assessing synthetic genetic interactions
     within and between cellular organizational units such as
     multi-protein complexes.

_U_s_a_g_e:

     modelSLGI(iMat, universe, interactome,  type="intM", perm=50)

_A_r_g_u_m_e_n_t_s:

    iMat: Adjacency matrix reporting genetic interactions. Each entry
          has value 0 or 1, representing positive or negative
          interaction of corresponding pairs of row and column.

universe: character vector of the names of the tested genes, e.g.,
          names of the genes on the synthetic genetic array (SGA) used
          by Tong et al.

interactome: Adjacency matrix where row are genes and columns are
          cellular organizational units. Each entry has value 0 or 1,
          for absence or presence of a gene in a complex.

    type: Character vector of value "intM" (Default) or "interactome"
          to either perform the test based on to the genetic
          interaction matrix or the interactome, respectively.

    perm: Number of permutations to apply. Default is 50.

_V_a_l_u_e:

     Interaction matrix between cellular organizational units.

_A_u_t_h_o_r(_s):

     N. LeMeur

_S_e_e _A_l_s_o:

     'getInteraction'

_E_x_a_m_p_l_e_s:

      data(ScISIC)
      data(Atong)
      data(SGA)
      model <-  modelSLGI(Atong, universe= SGA, interactome=ScISIC,
     type="intM", perm=2)
      

