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)

