estimatePPIErrorRates        package:ppiStats        R Documentation

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

     Estimate false positive and false negative error probabilities for
     direct protein interactions using a protein interaction graph gold
     standard

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

     estimatePPIErrorRates(matList,GSPos=NULL,GSNeg=NULL)

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

 matList: A named list of list. The names corresponds to a particular
          publication. Each element of the top list is a list of two
          matrices: 1. The adjacency matrix of the positive interaction
          datapoints. 2. The adjacency matrix of the tested interaction
          datapoints. The dimension names of these two matrices should
          be identical (an error will be thrown if this is not the
          case) where the rows are indexed by the bait proteins and the
          columns are indexed by the prey. The adjacency matrices are
          0,1 matrices where an 1 entry signifies either a positive
          interaction relationship or a positive tested relationship. A
          0 entry is then well defined.

   GSPos: A positive gold standard protein interaction graph given by
          its adjacency matrix. The dimension names of this matrix must
          be the same identifying system used for the dimension names
          for the matrices found within the matList parameter. An entry
          of one in this matrix indicates a positive interaction while
          an entry of zero is inconclusive.

   GSNeg: A negative gold standard protein interaction graph given by
          its adjacency matrix. The dimension names of this matrix must
          be the same identifying system used for the dimension names
          for the matrices found within the matList parameter. An entry
          of one in this matrix indicates a negative interaction while
          an entry of zero is inconclusive.

_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 matrix.

     The return value is an kx2 matrix where k is the length of
     matList. The first colum returns the estimated false positive
     error rates and the second column returns the estimated false
     negative error rates.

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

     T. Chiang and L. Wang

_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_.

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

     load(system.file("extdata", "intacty2hppMatrix.rda", package="ppiStats"))
     load(system.file("extdata", "PPIpos", package="ppiStats"))
     x = intacty2hppMatrix[c("EBI-389903","EBI-783101")]
     estimatePPIErrorRates(x, GSPos=PPIpos)

