getUniquePairs             package:SLGI             R Documentation

_F_i_n_d _u_n_i_q_u_e _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:

     'getUniquePairs' can find all the unique pairs from an interaction
     matrix and supplementary array genes, or finds only the unique
     pairs that shows positive interaction.

_U_s_a_g_e:

     getUniquePairs(iMat, respV = character(0), only = 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.

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

    only: has default value 'FALSE', if 'TRUE', then only reports the
          positively interacted pairs. 

_V_a_l_u_e:

     A data.frame with two or three columns.  The first two columns are
     the query gene name and the array gene name, respectively.  If
     'only' is 'TRUE', the third column shows the interaction status.

_A_u_t_h_o_r(_s):

     Z. Jiang

_S_e_e _A_l_s_o:

     'getSharedDomains'

_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
     getUniquePairs(intM,respV,only=FALSE)
     getUniquePairs(intM,respV,only=TRUE)
     getUniquePairs(intM,only=FALSE)
     getUniquePairs(intM,only=TRUE)

