checkComplex              package:ScISI              R Documentation

_F_u_n_c_t_i_o_n _t_o _c_h_e_c_k _a _l_i_s_t _o_f _p_r_o_t_e_i_n _c_o_m_p_l_e_x_e_s _w_r_t _S_c_I_S_I

_D_e_s_c_r_i_p_t_i_o_n:

     This function takes a named list of protein complexes (where each
     protein complex name indexes an item of the list and each list
     entry is the protein composition of the complex) and an
     interactome (in the bi-partite matrix representation) and checks
     to see if each complex of the list is either in the interactome, a
     sub-complex of some complex(es) of the interactome, or a
     super-complex of some complex(es) of the interactome.

_U_s_a_g_e:

     checkComplex(comps, interactome)

_A_r_g_u_m_e_n_t_s:

   comps: A named list of protein complexes. The names corresponds the
          protein complexes and the entries correspond to the complex
          composition

interactome: A bi-partite graph representation of some interactome

_D_e_t_a_i_l_s:

     This is another QC function to check the participation of certain
     protein complexes. The out-put will describe how the various
     protein complexes in question relate to the protein complexes of
     the interactome in question.

_V_a_l_u_e:

     A named list: 

   equal: A named character vector - the name equals the entry

  subset: A named char vector - the name is a subset of the entry

superset: A named char vector - the name is a superset of the entry

sameNameNotEqual: A named char vector - the name is equal to the name
          of the entry but the composition is not equal

_A_u_t_h_o_r(_s):

     T Chiang

_E_x_a_m_p_l_e_s:

     ##data(moreGO)
     ##data(ScISI)
     ##checkComplex(moreGO, ScISI)

