estimateCCMErrorRates        package:ppiStats        R Documentation

_E_s_t_i_m_a_t_e _f_a_l_s_e _p_o_s_i_t_i_v_e _a_n_d _f_a_l_s_e _n_e_g_a_t_i_v_e _e_r_r_o_r _p_r_o_b_a_b_i_l_i_t_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Estimate false positive and false negative error probabilities for
     complex comembership edges using a protein complex interactome
     gold standard

_U_s_a_g_e:

     estimateCCMErrorRates(m,GS,filterSystematic=TRUE,       
              obsPropThresh=1,SystematicpThresh=.01)

_A_r_g_u_m_e_n_t_s:

       m: The bait to prey data adjacency matrix. Baits index the rows
          and prey index the columns.

      GS: A gold standard protein complex interaction incidence matrix.
          Proteins index the rows and protein complexes index the
          columns. 

filterSystematic: A logical. If TRUE, all baits with with highly uneven
          directed degree will be filtered out of the data.

obsPropThresh: A numeric between 0 and 1. The proportion of tested
          proteins found within a protein complex needed to keep that
          protein complex within the gold standard set.

SystematicpThresh: A numeric between 0 and 1. The p-value threshold by
          which systematic errors are filtered.

_D_e_t_a_i_l_s:

     The model is described in the manuscript _Estimating node degree
     in bait-prey graphs._ by D. Scholtens et al.

_V_a_l_u_e:

     A list:

globalpTP: A numeric between 0 and 1.  Estimate of pTP.

globalpTPSE: A numeric.  Estimate of standard error of globalpTP
          estimate.

globalpFP: A numeric between 0 and 1.  Estimate of pFP.

 pTP95CI: A vector of length 2.  95 percent confidence interval upper
          and lower bounds for globalpTP estimate.

 pFP95CI: A vector of length 2.  95 percent confidence interval upper
          and lower bounds for globalpFP estimate.

nEligComplexes: A numeric.  Number of complexes from GS that met
          obsPropThresh criteria.

nEligBaits: A numeric. Total number of eligible baits in GS set.

nEligEdges: A numeric.  Total number of eligible edges in GS set.

nBaitsInComplexes: A vector.  Number of baits in each eligible complex.

complexSizes: A vector. Size of each complex in GS set.

_A_u_t_h_o_r(_s):

     T. Chiang and D. Scholtens

_R_e_f_e_r_e_n_c_e_s:

     Scholtens D, Chiang T, Huber W, Gentleman R.  Estimating node
     degree in bait-prey graphs. _Bioinformatics_.  To appear.

_E_x_a_m_p_l_e_s:

     data(Ho2002BPGraph)
     data(ScISIC)
     Ho2002mat = as(Ho2002BPGraph,"matrix")
     estimateCCMErrorRates(Ho2002mat,ScISIC)$globalpTP

