translateID             package:RpsiXML             R Documentation

_F_i_n_d_s _i_d_e_n_t_i_f_i_e_r_s _o_f _a _g_i_v_e_n _o_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     see 'translateID-methods'

_U_s_a_g_e:

     translateID(r, ...)

_A_r_g_u_m_e_n_t_s:

       r: An object of psimi25Graph, psimi25Hypergraph,
          psimi25Interactor or a list of 'psimi25Interactor'

     ...: the symbol of the ID to translate

_D_e_t_a_i_l_s:

     see 'translateID-methods'

_V_a_l_u_e:

     The object of the same class as the parameter

_A_u_t_h_o_r(_s):

     Jitao David Zhang <j.zhang@dkfz.de>

_S_e_e _A_l_s_o:

     see 'translateID-methods'

_E_x_a_m_p_l_e_s:

     xmlDir <- system.file("/extdata/psi25files",package="RpsiXML")

     hprdxml <- file.path(xmlDir, "hprd_200709_test.xml")
     hprdSet <- parsePsimi25Interaction(hprdxml, HPRD.PSIMI25)

     it <- interactors(hprdSet)[[1]]
     translateID(it, "uniprot")
     translateID(it, "entrezgene")

     ##Not run
     intactxml <- file.path(xmlDir, "intact_2008_test.xml")
     intactSet <- parsePsimi25Interaction(intactxml, INTACT.PSIMI25)
     intactGraph <- psimi25XML2Graph(intactxml, INTACT.PSIMI25)
     intactGraphNew <- translateID(intactGraph,"sourceId")## translate the nodes of the graph to another identifier
                                   
     intactSetInteractors <- interactors(intactSet)
     intactXrefExample <- xref(intactSetInteractors[[1]])
     translateID(intactSetInteractors,"intact")
     translateID(intactSetInteractors[[1]],"intact")

     intactComplexxml <- file.path(xmlDir,"intact_complexSample.xml")
     intactComplexSet <- parsePsimi25Complex(intactComplexxml, INTACT.PSIMI25)
     intactComplexGraph <- psimi25XML2Graph(intactComplexxml, INTACT.PSIMI25, type="complex")
     translateID(intactComplexGraph, "intact", "P49432")
     translateID(intactComplexGraph, "intact", NA)
     ## End(Not run)

