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)

