yNameTAP complexes         package:apComplex         R Documentation

_T_A_P _d_a_t_a _c_o_m_p_l_e_x _e_s_t_i_m_a_t_e_s _u_s_i_n_g _s_t_a_n_d_a_r_d _g_e_n_e _n_a_m_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(yNameTAP)

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

     These are the results from an analysis of the TAP data (Gavin et
     al., 2002) 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 .995, and Beta=-0.2 for externally derived similarity measure
     based on Gene Ontology cellular component annotation (see
     Scholtens and Gentleman (2004)).

     'yNameTAP' contains 260 multi-bait-multi-edge complex estimates.

_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.  Bioinformatics 21, 3548-3557 (2005).

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

     Gavin, et al. Functional organization of the yeast proteome by
     systematic analysis of protein complexes.  Nature 415, 141-147
     (2002).

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

     'TAP','TAPgraph,\code{yTAP},\code{findComplexes}'

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

     data(yNameTAP)
     yNameTAP[1:10,1:3]

