getComponents          package:gene2pathway          R Documentation

_K_E_G_G _p_a_t_h_w_a_y _i_n_f_o_r_m_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     1. get connected pathway components; 2. get all elements of a
     given pathway; 3. color certain elements in a pathway.

_U_s_a_g_e:

     getComponents(pathway.id)

     get.elements.by.pathway(pathway.id)

     color.pathway.by.elements(pathway.id, elements)

_A_r_g_u_m_e_n_t_s:

pathway.id: KEGG pathway ID, e.g. "path:hsa04012"

elements: KEGG element IDs: character vector of numbers

_D_e_t_a_i_l_s:

     All functions use the KEGG SOAP service.

_V_a_l_u_e:

     getComponents: a list with the entries 

 geneIDs: Entrez gene IDs mapping to each pathway component

 elemIDs: KEGG element IDs mapping to each pathway component


     get.elements.by.pathway: list, see <URL
     http://www.genome.jp/kegg/soap/doc/keggapi_manual.html> for
     details

     color.pathway.by.elements: an URL of a colored gif file, see <URL
     http://www.genome.jp/kegg/soap/doc/keggapi_manual.html> for
     details

_A_u_t_h_o_r(_s):

     Holger Froehlich

_E_x_a_m_p_l_e_s:

     ## Not run: 
       comp = getComponents("path:hsa04020") # get all connected components
       color.pathway.by.elements("path:hsa04020", comp$elemIDs[[1]]) # mark first component
     ## End(Not run)

