psimi25Hypergraph-class       package:RpsiXML       R Documentation

_C_l_a_s_s "_p_s_i_m_i_2_5_H_y_p_e_r_g_r_a_p_h"

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

     Class to present PSI-MI 2.5 XML data as hypergraph. Proteins are
     projected as hypergraph nodes and complex composition as
     hyperedges.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'psimi25XML2Graph'

_S_l_o_t_s:


     '_i_n_t_e_r_a_c_t_o_r_s': Object of class '"matrix"', Object of class
          '"matrix"', interactor information in a matrix, Each row
          represents one interactor. Source IDs are used as row names.
          Each column represents one annotation.  Annotations include:
          UniProt ID, short label, organism name, and NCBI taxonomy ID.
          Only those interactors which are  the nodes of the
          psimi25Graph is given.

_E_x_t_e_n_d_s:

     Class 'Hypergraph', directly

_M_e_t_h_o_d_s:


     _i_n_i_t_i_a_l_i_z_e 'signature(.Object = "psimi25Hypergraph")' 

     _s_h_o_w 'signature(object = "psimi25Hypergraph")': show method,print
          complex and protein number

     _i_n_t_e_r_a_c_t_o_r_s 'signature(object = "psimi25Hypergraph")': list of
          'psimi25Interactor' objects, providing full information of
          complex members

     _e_d_g_e_L_a_b_e_l 'signature(object = "psimi25Hypergraph")': returns
          complex names (as hyperedge label), as a character vector

     _h_y_p_e_r_e_d_g_e_N_o_d_e_s 'signature(object = "Hypergraph")': returns a list
          of characters: names of the list are complex names and
          character vector in each list item are the members of that
          complex

     _c_o_m_p_l_e_x_e_s 'signature(object = "psimi25Hypergraph")': a wrapper of
          'hyperedgeNodes'

     _t_r_a_n_s_l_a_t_e_S_o_u_r_c_e_I_D 'signature(r = "psimi25Hypergraph")': translate
          source ID into other IDs 

     _n_u_m_I_n_t_e_r_a_c_t_o_r_s 'signature(r = "psimi25Hypergraph")': returns the
          number of proteins

     _i_n_t_e_r_a_c_t_o_r_I_n_f_o 'signature(r = "psimi25Hypergraph")': returns a
          data frame containing essential information of the
          interactors

     _n_u_m_E_d_g_e_s 'signature(r = "psimi25Hypergraph")': returns the number
          of complexes

     _r_e_v_I_n_c_i_M_a_t 'signature(r = "matrix")': returns the hypergraph built
          from the incidence matrix


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

     Tony Chiang <tchiang@ebi.ac.uk> , Jitao David Zhang
     <j.zhang@dkfz.de>

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

     'psimi25XML2Graph','S4classpsimi25Graph-class'

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

     xmlDir <- system.file("/extdata/psi25files",package="RpsiXML")
     intactComplexxml <- file.path(xmlDir,"intact_complexSample.xml")
     pc1 <- buildPCHypergraph(intactComplexxml, INTACT.PSIMI25)

     ## print number of proteins and complexes (edges)
     numNodes(pc1)
     ## the same as numInteractors(pc1)
     numEdges(pc1)

     ## print proteins (nodes)
     nodes(pc1)[1:3]

     ## print complex names
     edgeLabel(pc1)[1:3]

     ## print complexes (not so informative with 'hyperedges')
     hyperedges(pc1)[1:3]
     ## better with 'complexes' or 'hyperedgeNodes'
     complexes(pc1)[1:3]

     ## get interactor detailed information
     interactors(pc1)[[1]]

