getInteraction             package:SLGI             R Documentation

_C_o_u_n_t _g_e_n_e_t_i_c _i_n_t_e_r_a_c_t_i_o_n_s _w_i_t_h_i_n _a_n_d _b_e_t_w_e_e_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 number of genetic interactions within and between the
     elements of the interactome.

_U_s_a_g_e:

     getInteraction(iMat, universe, interactome)

_A_r_g_u_m_e_n_t_s:

    iMat: Interaction matrix. Each entry has value 0 or 1, representing
          positive or negative interaction of corresponding pairs of
          row and column, respectively.

universe: Character vector of gene names, e.g., array genes used in
          synthetic genetic array experiments (SGA)

interactome: Adjacency matrix where row are gene names and columns are
          cellular organizational units. 

_V_a_l_u_e:

     The returned value is a list of 2 matrices: 

   bwMat: A interaction matrix that corresponds to the  cellular
          organizational units interaction matrix where row and columns
          a organizational units names and the value inside the matrix
          are the number of genetic interactions they share.

     CDs: Subset of the input interactome that shares interactions.

_A_u_t_h_o_r(_s):

     N. LeMeur

_E_x_a_m_p_l_e_s:

     ##Create the genetic interaction matrix
     gInt <- sample(c(0, 1), 25, TRUE)
     iMat  <- matrix(gInt, nrow=5, ncol=5, dimnames=list(letters[1:5],letters[4:8]))

     ##Create the interactome
     cInt <- sample(c(0,1),30, TRUE)
     interactome  <- matrix(cInt, nrow=6, ncol=5,dimnames=list(letters[2:7],LETTERS[1:5]))

     ## Reduce the genetic interaction matrix to match the gene present in
     ## the interactome
     reducediMat <- gi2Interactome(iMat, interactome)

     ## Get the interaction
     prey <- letters[1:20]
     myInteraction <- getInteraction(reducediMat, prey, interactome)

