buildPCHypergraph          package:RpsiXML          R Documentation

_B_u_i_l_d _p_r_o_t_e_i_n _c_o_m_p_l_e_x _h_y_p_e_r_g_r_a_p_h _f_r_o_m _P_S_I-_M_I _2._5 _f_i_l_e_s

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

     The protein complexes can be represented by hypergraph models,
     with proteins as nodes and complexes as hypergraphs. This function
     builds protein complex hypergraph from one or more PSI-MI 2.5
     files (complex mode), with the option to split the dataset by
     organism name or taxonomy ID of the complexes.

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

     buildPCHypergraph(xmlFiles, psimi25source, split.by = c("none", "organismName", "taxId"), ...)

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

xmlFiles: PSI-MI 2.5 files, must be of complex mode. 

psimi25source: PSI-MI 2.5 source indicator, for example INTACT.PSIMI25
          for files from IntAct database

split.by: The qualifier to split the dataset, 'none' specifies not to
          split the dataset, 'organismName' and 'taxId' splits the
          dataset according to organism name or taxonomy ID
          respectively. In the case of splitting, the results are a
          list of hypergraphs indexed by respective split qualifier

     ...: other parameters passed to 'parsePsimi25Complex'

_D_e_t_a_i_l_s:

     See 'psimi25Hypergraph-class' for the use of resulting hypergraphs
     and examples.

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

     In case the dataset is not split (by setting the option 'split.by'
     as 'none', the result is a 'psimi25Hypergraph-class' object. If
     the dataset was split, a list of 'psimi25Hypergraph-class' is
     returned, which is indexed by either the organism name or the
     taxonomy ID.

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

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

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

     'psimi25Hypergraph-class' for the use of hypergraph objects,
     'separateXMLDataByExpt' for similar functionality but for
     interaction mode files

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

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

     pc2 <- buildPCHypergraph(intactComplexxml,
     INTACT.PSIMI25,split.by="organismName")

     pc2[2]
     complexes(pc2[[2]])[1:3]

