depthmat               package:GraphAT               R Documentation

_M_a_t_r_i_c_e_s _o_f _d_e_p_t_h _o_f _a_s_s_o_c_i_a_t_i_o_n _f_o_r _p_a_i_r_s _o_f _Y_E_A_S_T _g_e_n_e_s _w_i_t_h
_r_e_s_p_e_c_t _t_o _e_a_c_h _o_f _t_h_e _B_P,_C_C _a_n_d _M_F _o_n_t_o_l_o_g_i_e_s _o_f _t_h_e _G_O _d_a_t_a_b_a_s_e

_D_e_s_c_r_i_p_t_i_o_n:

     This matrix of depths is used to obtain the predictome data in the
     paper. This is a symmetric matrix, where the i,j element
     corresponds to is the maximum depth of all annotations shared by
     genes i and j. Note that depth of a term in a specific Gene
     Ontology (BP, CC, MF) is defined as the shortest path between the
     term and the root node, where distance between nodes is measured
     by the number of edges traversed. Row labels of the matrix can be
     obtained by the row.names() function

_U_s_a_g_e:

     data(depthmatBP)

_F_o_r_m_a_t:

     Each of three matrices, namely depthmatBP.rda, depthmatCC.rda,
     depthmatMF.rda is a symmetric matrix whose rows and columns
     correspond to specific YEAST genes (see row labels using
     row.names()). The i,j entry of each matrix refers to the maximum
     depth shared by genes i and j under each of the BP, CC and MF
     ontlogies respectively

_S_o_u_r_c_e:

     <URL: http://www.geneontology.org>

_R_e_f_e_r_e_n_c_e_s:

_E_x_a_m_p_l_e_s:

      
     data(depthmatBP)
     print(row.names(depthmatBP)[1:10])

