ROC                 package:cellHTS                 R Documentation

_C_r_e_a_t_e_s _a_n _o_b_j_e_c_t _o_f _c_l_a_s_s "_R_O_C" _w_h_i_c_h _c_a_n _b_e _p_l_o_t_t_e_d _a_s _a _R_O_C _c_u_r_v_e

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

     The function 'ROC' construct an object of S3 class 'ROC', which
     represents a receiver-operator-characteristic curve, from the data
     of the annotated positive and negative controls in a scored
     'cellHTS' object.

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

     ROC(x, positives, negatives)
     ## S3 method for class 'ROC':
     plot(x, col="darkblue", type="l", main = "ROC curve", ...)
     ## S3 method for class 'ROC':
     lines(x, ...)

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

       x: a 'cellHTS' object that has already been scored (see
          details).

positives: a list or vector of regular expressions specifying the name
          of the positive controls.  See the details for the argument
          'posControls' of 'writeReport' function.

negatives: a vector of regular expressions specifying the name of the
          negative controls.  See the details for the argument
          'negControls' of 'writeReport' function.

     col: the graphical parameter for color; see 'par' for details.

    type: the graphical parameter giving the type of plot desired; see
          'par' for details.

    main: the graphical parameter giving the desired title of plot; see
          'par' for details.

     ...: other graphical parameters as in 'par' may be also passed as
          arguments.

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

     The 'cellHTS' object 'x' must contain a slot called 'score', and
     selection proceeds from large to small values of this score.
     Furthermore, 'x' is expected to contain positive and negative
     controls annotated in the slot 'wellAnno' with the values of the
     arguments 'positives' and 'negatives', respectively. If the assay
     is a two-way experiment, 'positives' should be a list with
     components 'act'  and 'inh', specifying the name of the
     activators, and inhibitors, respectively. In this case, the ROC
     cureve is constructed based on the absolute values of 'x$score'.

_V_a_l_u_e:

     An S3 object of class 'ROC'. There are methods 'plot.ROC' and
     'lines.ROC'.

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

     Ligia P. Bras ligia@ebi.ac.uk

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

         data(KcViabSmall)
         ## Not run: 
         x <- normalizePlates(KcViabSmall, normalizationMethod="median", zscore="-")
         x <- summarizeReplicates(x)
         y <- ROC(x)
         plot(y)
         lines(y)
         
     ## End(Not run)

