ROCDATA                package:msbase                R Documentation

_T_r_a_n_s_f_o_r_m_a_t_i_o_n _a_n_d _o_t_h_e_r _f_a_c_t_o_r_s _o_f _t_h_e _p_a_i_r_w_i_s_e _p_e_a_k-_l_i_s_t_s
_C_o_m_p_a_r_s_i_o_n _P_r_o_c_e_s_s

_D_e_s_c_r_i_p_t_i_o_n:

     Scores of the binary and intensity based measures for PMF and
     MS/MS datasets. The file contains the sensitivity and specificity
     PAUC obtained for each set of factors. In addition it contains the
     AUC and max(sum(specificity+sensitivity)). For an analysis of
     variance, to determine the best performing measures see the Sweave
     file varan.Rnw in the doc directory of the package.

_U_s_a_g_e:

     data(pmf.binary); data(pmf.intensity);data(msms.binary);data(msms.intensity)

_F_o_r_m_a_t:

     A dataframe with 10 columns and 96 (Binary) or rows.

_D_e_t_a_i_l_s:

     Column names and they content.

        *  ABBREV - abreviation of CP

        *  Measure - Measure (dissimilarity measure)

           *  Binary - measures.

              *  fm - Fowlkes Mallows

              *  hg - Huberts Gamma

              *  rmi - relative mutual information

              *  gower - gower coefficient

           *  Intensity -  based measures.

              *  cov - Covariance

              *  soai - sum of agreeing intensities

              *  euclidean - euclidean distance

              *  manhattan - Manhattan distance

              *  canberra - Canberra distance

              *  simindex - similarity index

              *  dotprod - dot product measure

        *  Trans (intensity transformation)

           *  N - raw data

           *  S - square root transformation

           *  L - log transformation

           *  R - ranks of intensities

        *  Scale - scaling of peak intensities

           *  T - total ion count scaling

           *  N - vector length

           *  S - root mean square

           *  Z - z-score        

        *  theta - weigth of non-matching peaks

           *  0.5                         

           *  1                           

           *  2   

        *  Weight - weighting of measurement accuracy

           *  M - without non-crossing matching                  

           *  W - with non-crossing matching     

        *  Noncross (non-crossing matching)

           *  A - the non-crossing matching was determined

           *  O - the non-crossing matching was not determined

        *  Length - length of aligned PLs

           *  N=0

           *  N=250 (PMF) ; N=800 (MSMS)

        *  AUC - Area under the reveiver operator characteristic curve.

        *  MaxSSp - Maxiumum of sensitivity + specificity on the ROC
           curve.

        *  FPPAUC - specificity PAUC.

        *  TPPAUC - sensitivity PAUC

_S_o_u_r_c_e:

_R_e_f_e_r_e_n_c_e_s:

     Wolski et al. "Transformation and other factors of the peptide MS
     peak-list comparsion process"(2005) See doc directory of this
     package

_E_x_a_m_p_l_e_s:

     data(pmf.binary)
     data(pmf.intensity)
     data(msms.binary)
     data(msms.intensity)

