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)

