unWantedComp              package:ScISI              R Documentation

_A _f_u_n_c_t_i_o_n _t_o _m_a_n_u_a_l_l_y _r_e_m_o_v_e _p_r_o_t_e_i_n _c_o_m_p_l_e_x_e_s _f_r_o_m _s_o_m_e _i_n
_s_i_l_i_c_o _i_n_t_e_r_a_c_t_o_m_e

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

     This function takes in an in silico interactome by its bipartite
     graph representation and a character vector of complex ID's. The
     function parses through the column names of the in silico
     interactome and removes those columns whose names are found in the
     character vector.

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

     unWantedComp(ISI, unwantedComplex = c("GO:0000262", "GO:0000228",
     "GO:0000775", "GO:0010008", "GO:0005792", "GO:0005768", "GO:0005769",
     "GO:0005770", "GO:0005777", "GO:0005844", "GO:0001400"), unwantedGenes =
     c("RNA_TLC1", "SNRNA_NME1","RNA_RNASE-P"))

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

     ISI: The in silico interactome as a bipartite graph

unwantedComplex: A character vector. Each entry is a protein complex id
          for which should be removed from the interactome.

unwantedGenes: A character vector of gene names that will be deleted
          from the row indexing set of the in silico interactome.

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

     An incidence matrix. A new matrix with those columns indexed by
     unwantedComplex removed. It will also remove any protein which is
     now no longer contained in any protein complex.

_N_o_t_e:

     The entries of unwantedComplex must be found in the column names
     of ISI, otherwise, they will not be removed. This is especially
     important since there are many id's that index the same protein
     complex.

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

     T. Chiang

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

     mips = getMipsInfo()
     go = getGOInfo()
     mipsM = createMipsMatrix(mips)
     goM = createGOMatrix(go)
     mips2go = runCompareComplex(mipsM, goM, byWhich = "ROW")
     merged = mergeBGMat(mipsM, goM, mips2go$toBeRm)
     ISI = unWantedComp(merged)

