ppiInteract             package:PCpheno             R Documentation

_T_e_s_t _t_h_e _a_s_s_o_c_i_a_t_i_o_n _b_e_t_w_e_e_n _A_P-_M_S _d_a_t_a _a_n_d _p_h_e_n_o_t_y_p_e

_D_e_s_c_r_i_p_t_i_o_n:

     Test the association between AP-MS data and phenotype data via a
     graph and permutation model.

_U_s_a_g_e:

     ppiInteract(genename, expGraph, bait, prey, perm=10)

_A_r_g_u_m_e_n_t_s:

genename: Genes associated to a phenotype

expGraph: A graphNEL object (a direct graph instance of class'graph').
          The nodes are the union of viable baits (VB) and viable prey
          (VP) of the experiment (see package _ScISI_)

    bait: Proteins which was sampled as a bait in the binary
          relationship

    prey: Proteins which was sampled as a prey in the binary
          relationship

    perm: Number of permutation

_V_a_l_u_e:

     The returned value is a list: 

Observed: Observed values

Expected: Expected values after each permutation

_A_u_t_h_o_r(_s):

     R. Gentleman and N. LeMeur

_S_e_e _A_l_s_o:

     _ScISI_

_E_x_a_m_p_l_e_s:

     data(ScISI)
     data(essglist)
     s1 <- ppiInteract(names(essglist), Gavin2002BPGraph, viableBaits[[8]],
            viablePrey[[8]], perm=10)

