byComplex                package:SLGI                R Documentation

_E_v_a_l_u_a_t_e _p_r_o_t_e_i_n _c_o-_m_e_m_b_e_r_s_h_i_p _w_i_t_h_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:

     Count the protein co-members of one (or more) cellular
     organizational units such as complex(es). This co-membership can
     be characterized by a synthetic lethal interaction if bpL is the
     list of observed synthetic lethal interactions or it can be
     characterized by the number of all the expected interactions
     within that complexes if bpL is all the interactions tested.

_U_s_a_g_e:

     byComplex(bpL,interactome)

_A_r_g_u_m_e_n_t_s:

     bpL: List of tested genes (or reported as synthetic lethal) per
          bait.

interactome: Adjacency matrix where the rows are the genes and the
          columns represent the cellular organizational units, e.g.,
          'ScISI'

_V_a_l_u_e:

     Vector of the number of genes(proteins) co-member in one or more
     biological complexes or pathways.

_A_u_t_h_o_r(_s):

     N. LeMeur and R. Gentleman

_S_e_e _A_l_s_o:

     'withinComplex'

_E_x_a_m_p_l_e_s:

       data(ScISIC)
       data(AtongPair)
       pairSL <-  AtongPair[ AtongPair[,3],]
       SLlist <- split(as.character(pairSL[,2]),as.character(pairSL[,1]))
       ##Number of synthetic lethal pairs within the same complexe 
       bySL <-byComplex(SLlist, ScISIC)
      

