getTestedPairs             package:SLGI             R Documentation

_F_i_n_d _i_n_t_e_r_a_c_t_i_n_g _a_n_d  _n_o_n-_i_n_t_e_r_a_c_t_i_n_g _t_e_s_t_e_d _p_a_i_r_s _f_r_o_m _a_n _g_e_n_e_t_i_c _i_n_t_e_r_a_c_t_i_o_n _m_a_t_r_i_x.

_D_e_s_c_r_i_p_t_i_o_n:

     'getTestedPairs' find all the pairs from an interaction matrix and
     a list of tested genes.

_U_s_a_g_e:

     getTestedPairs(iMat, respV)

_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.

   respV: Character vector of all gene names that were tested (found to
          interact or not) 

_V_a_l_u_e:

     A data.frame with 4 columns: 

   query: gene names of the query genes

   array: gene names og the tested genes (e.g., array genes)

interact: numeric vector of the number of observed interactions (0: no
          interaction; 1: one interaction; 2: two interactions when the
          query genes were also on the array)

   recip: logical to indicate whether the reported genes were both
          query and array genes (TRUE: both genes were query and array
          genes)

     .

_A_u_t_h_o_r(_s):

     N. LeMeur

_S_e_e _A_l_s_o:

     'getSharedDomains' 'getUniquePairs'

_E_x_a_m_p_l_e_s:

     intM <- c(0,1,0,0,1,1,0,0,1,0,0,1,1,0,1,0)
     dim(intM) <- c(4,4)
     dimnames(intM) <- list(c("p1","p2","p3","p4"),c("p1","p3","p5","p7") )
     respV <- c("p6","p8")
     intM
     getTestedPairs(intM,respV)

