test2Interact              package:SLGI              R Documentation

_S_u_m_m_a_r_i_z_e _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 _o_r _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:

     Summarize the genetic interactions within one cellular
     organizational unit or between 2 cellular organizational units.

_U_s_a_g_e:

     test2Interact(iMat, tMat, interactome)

_A_r_g_u_m_e_n_t_s:

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

    tMat: Adjacency matrix of tested object. Each entry has value 0 or
          1, representing the fact that the corresponding pairs of row
          and column have been tested for interaction or not.

interactome: Adjacency matrix where  row are gene names and columns are
          cellular organizational units names. Each entry has value 0
          or 1, for absence or presence of a gene in the complex.

_V_a_l_u_e:

     the return value is a data.frame with 6 columns.

unit1, unit2: cellular organizational units tested and interacting

  tested: Number of interactions tested between unit1 and unit2

interact: Number of interactions found between unit1 and unit2

sizeC1, sizeC2: Number of genes in  unit1 and unit2

_A_u_t_h_o_r(_s):

     N. LeMeur

_E_x_a_m_p_l_e_s:

     set.seed(123)
     ##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]))

     ## Create cellular organizational units interaction matrix
     gInt <- sample(c(1:8), 25, TRUE)
     gInt  <- matrix(gInt, nrow=5, ncol=5, dimnames=list(LETTERS[1:5],LETTERS[1:5]))

     ## All interactome tested
     gTest <- matrix(sample(c(0:3), 25, TRUE), nrow=5, ncol=5)
     gTested <- gInt+gTest

     val <- test2Interact(iMat=gInt, tMat=gTested, interactome=interactome)

