HMSPCI complexes          package:apComplex          R Documentation

_H_M_S_P_C_I _d_a_t_a _c_o_m_p_l_e_x _e_s_t_i_m_a_t_e_s

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

     Affiliation matrices with rows corresponding to proteins and
     columns corresponding to complexes.

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

     data(MBMEcHMSPCI)
     data(SBMHcHMSPCI)
     data(UnRBBcHMSPCI)

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

     These are the results from an analysis of the HMS-PCI data (Ho et
     al., 2002) described by Scholtens and Gentleman (2004) and
     Scholtens, Vidal, and Gentleman (submitted).  These estimates were
     constructed using 'findComplexes' with a sensitivity parameter of
     .75, specificity of .99, and Beta=-0.2 for externally derived
     similarity measure based on Gene Ontology cellular component
     annotation (see Scholtens and Gentleman (2004)).

     'MBMEcHMSPCI' contains 242 multi-bait-multi-edge complex
     estimates. 'SBMHcHMSPCI' contains 437 single-bait-multi-hit
     complex estimates. 'UnRBBcHMSPCI' contains 329 unreciprocated
     bait-bait complex estimates.  These data are also available at
     http://www.bioconductor.org/Docs/Papers/2003/apComplex.

_S_o_u_r_c_e:

     Scholtens D and Gentleman R.  Making sense of high-throughput
     protein-protein interaction data.  Statistical Applications in
     Genetics and Molecular Biology 3, Article 39 (2004).

     Scholtens D, Vidal M, and Gentleman R.  Local modeling of global
     interactome networks.  Submitted.

_R_e_f_e_r_e_n_c_e_s:

     Ho, et al. Systematic identification of protein complexes in
     Saccharomyces cerevisiae by mass spectrometry.  Nature 415,
     180-183 (2002).

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

     'HMSPCI','HMSPCIgraph,\code{findComplexes}'

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

     data(MBMEcHMSPCI)
     MBMEcHMSPCI[1:4,1:4]
     which(MBMEcHMSPCI[,"MBME1"]==1)

