densityEstimate           package:PCpheno           R Documentation

_O_b_s_e_r_v_e_d _v_e_r_s_u_s _E_x_p_e_c_t_e_d _R_a_t_i_o_s

_D_e_s_c_r_i_p_t_i_o_n:

     Function to calculate the ratio of genes that characterize a
     phenotype (observed) among the genes that characterize a
     biological complex versus the ratio of a set of randomly sampled
     genes (expected) among the genes that characterize a biological
     complex.

_U_s_a_g_e:

     densityEstimate(genename,interactome,perm)

_A_r_g_u_m_e_n_t_s:

genename: Character vector of the gene names that characterize a
          specific phenotype.

interactome: Contingency matrix of genes (rows) and biological
          complexes (columns) (see package _ScISI_) 

    perm: Numeric vector indicating the number of simulations to run to
          compute the expected ratios.

_V_a_l_u_e:

     List of observed and simulated ratios.

_A_u_t_h_o_r(_s):

     N. LeMeur

_E_x_a_m_p_l_e_s:

      data(ScISI)
      data(essglist)
      essential <- names(essglist)
      ScISI <- as.matrix(ScISI)
       ratio<- densityEstimate(genename=essential,interactome=ScISI,perm=50)

