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="pos", negatives = "neg")
     ## S3 method for class 'ROC':
     plot(x, col="darkblue", type="l", ...)
     ## 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 character string corresponding to the name used to
          annotate the positive controls in the cellHTS object.

negatives: a character string corresponding to the name used to
          annotate the negative controls in the cellHTS object.

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

    type: the graphical parameter giving the type of plot desired; 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.

_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):

     W. Huber huber@ebi.ac.uk

_E_x_a_m_p_l_e_s:

      datadir = system.file("KcViabSmall", package = "cellHTS")
      x = readPlateData("Platelist.txt", "KcViabilitySmall", path=datadir)
      confFile = system.file("KcViabSmall", "Plateconf.txt", package="cellHTS")
      logFile  = system.file("KcViabSmall", "Screenlog.txt", package="cellHTS")
      descripFile  = system.file("KcViabSmall", "DESCRIPTION.txt", package="cellHTS")
      x = configure(x, confFile, logFile, descripFile)
      x = normalizePlateMedian(x, zscore="-")
      x = summarizeReplicates(x)
      y = ROC(x)
      plot(y)
      lines(y)

