sharedInt                package:SLGI                R Documentation

_L_i_s_t _s_h_a_r_e_d _g_e_n_e_t_i_c _i_n_t_e_r_a_c_t_i_o_n_s _b_e_t_w_e_e_n _g_e_n_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     List shared interactions and cellular organizational units names
     between genes.

_U_s_a_g_e:

     sharedInt(pairL, interactome, threshold=0)

_A_r_g_u_m_e_n_t_s:

   pairL: Dataframe with 3 columns. The first columns are the pair of
          genes tested i.e., the query and array genes. The third
          columns in a logical: TRUE when the 2 genes genetically
          interact and FALSE when they do not.(see 'AtongPair' dataset
          as example)

interactome: Adjacency matrix where  row are gene names and columns are
          cellular organizational units names. Each entry has value 0
          or 1, for absence or presence of a gene in the complex.

threshold: Numeric. Indicate the minimum number of interactions that 2
          genes must share

_V_a_l_u_e:

     The return value is a list. Each element of the list has for name
     2 genes that genetically interact. Each element of the list
     corresponds to the list of cellular organizational units where the
     interacting genes are found (independently or together).

_A_u_t_h_o_r(_s):

     N. LeMeur

_E_x_a_m_p_l_e_s:

     ## Synthetic genetic interactions 
     dat <- data.frame("query" = LETTERS[1:5], "array" = LETTERS[2:6], "interact" = as.logical(sample(c(TRUE, FALSE), 5, TRUE)))
     ## interactome
     interA <- matrix(sample(c(0, 1), 30,TRUE), nrow=6, ncol=5,dimnames = list(LETTERS[1:6], letters[1:5]))

     sharedInt(dat, interA, threshold=1)

