congruence               package:SLGI               R Documentation

_C_a_l_c_u_l_a_t_e _c_o_n_g_r_u_e_n_c_e _s_c_o_r_e _b_e_t_w_e_e_n _p_a_i_r_s _o_f _o_f _g_e_n_e_s _s_h_a_r_i_n_g
_p_a_t_t_e_r_n _o_f _s_y_n_t_h_e_t_i_c _g_e_n_e_t_i_c _i_n_t_e_r_a_c_t_i_o_n_s
(_Y_e _e_t _a_l. (_2_0_0_5)).

_D_e_s_c_r_i_p_t_i_o_n:

     The 'congruence' score represents the number of common synthetic
     genetic interacting partners between two genes. The higher is the
     score the more overlap there is between the synthetic genetic
     partners of those genes.

_U_s_a_g_e:

     congruence(iMat, sharedInt, mode="query", universe, padjust=FALSE)

_A_r_g_u_m_e_n_t_s:

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

sharedInt: numeric vector representing the number of common genetic
          interactions between a pair of query or target genes. See
          'getSharedInteraction' for more details

    mode: character vector of value "query" or "target"

universe: total number of genes tested

 padjust: adjust by the number of genes tested that show at least one
          synthetic genetic interaction.

_V_a_l_u_e:

     A numeric vector of the congruence score values.

_A_u_t_h_o_r(_s):

     N. LeMeur

_R_e_f_e_r_e_n_c_e_s:

     Ye P. et al. (2005). Gene function prediction from congruent
     synthetic lethal interactions in yeast. Molecular Systems Biology
     1:2005.0026.

_S_e_e _A_l_s_o:

     'getSharedInteraction'

_E_x_a_m_p_l_e_s:

     intM <- matrix(c(0,1,0,0,1,1,1,0,1,1,1,1,1,0,1,1),
                     nrow=4, ncol=4, 
                     dimnames=list(c("p1","p2","p3","p4"),
                       c("p1","p3","p5","p7")))
     sharedInt <- getSharedInteraction(intM)
     score <- congruence(intM, sharedInt, mode="query", universe=15, padjust=FALSE)

