byComplex                package:SLGI                R Documentation

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_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)
      

