goTools               package:goTools               R Documentation

_R_e_f_e_r_e_n_c_e _G_O _n_o_d_e_s _l_i_s_t.

_D_e_s_c_r_i_p_t_i_o_n:

     The function 'EndNodeList' builds the default end node list used
     in 'ontoCompare'. 'CustomEndNodeList' helps you build a list of
     children nodes starting from a GO id of interest.

_U_s_a_g_e:

     EndNodeList()
     CustomEndNodeList(id,rank=1)

_A_r_g_u_m_e_n_t_s:

      id: Valid GO id: "GO:XXXXXXX".

    rank: Number of levels of children of the GO DAG under id you want
          to add to your nodes list.

_V_a_l_u_e:

     'EndNodeList' returns a vector of all GO ids 1 level below
     MF("GO:0003674"), BP("GO:0008150") and CC("GO:0005575"). MF, BP
     and CC nodes are included. 'CustomEndNodeList' returns a vector of
     all GO ids children of 'id', 'rank' levels below it.

_A_u_t_h_o_r(_s):

     Yee Hwa (Jean) Yang, Agnes Paquet

_S_e_e _A_l_s_o:

     'ontoCompare'

_E_x_a_m_p_l_e_s:

     ## Examples use the probeID dataset. For description type ? probeID.
     ## library(GO.db)
     ## EndNodeList()
     ## MFendnode <- CustomEndNodeList("GO:0003674", rank=2)

     ## Example (not run)
     ## data(probeID)
     ## ontoCompare(affylist, probeType="hgu133a", endnode=MFendnode, goType="MF")

