proBin               package:flowStats               R Documentation

_P_r_o_b_a_b_i_l_i_t_y _b_i_n_n_i_n_g - _a _m_e_t_r_i_c _f_o_r _e_v_a_l_u_a_t_i_n_g _m_u_l_t_i_v_a_r_i_a_t_e _d_i_f_f_e_r_e_n_c_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function divides the flowframe events into bins such that
     each bin contains the same number of events. The number of events
     falling into each bin can then be compared across the control and
     test samples using statistical methods such as the Chi-squared
     test.

_U_s_a_g_e:

     proBin(m, minEvents)

_A_r_g_u_m_e_n_t_s:

       m: An object of class 'flowFrame'

minEvents: The 'minEvents' The minimum number of events in each bin.
          (i.e. the termination criterion for the probability binning
          algorithm)

_D_e_t_a_i_l_s:

     The 'flowSet' is first filtered using a 'rectangleGate' and the
     'norm2Filter' is subsequently fitted to the remaining subset.

_V_a_l_u_e:

     A list with items:

  table : A 'data.frame' that stores information regarding each node of
          the tree generated during each stage of the probability
          binning algorithm.  Each row in the table represents a node,
          the first row representing the original 'flowFrame' matrix.

          The dataIndx column provides indexes for retrieving the
          matrices during each stage of the binning process from the
          enviroment 'data' .

          The parent field indicates the row number in the table that
          holds the parent information for the corresponding node.

          The left and right columns indicates the row numbers in the
          table that stores information regarding the children of that
          particular node. The leaf nodes that hold the binned data can
          be identified by the nodes with the left of right values of
          zero( ie. no children nodes)

          The visited column is used internally by the algorithm to
          check if a particular node has been visited during the
          computation process.

   data : An enviroment in which the matrices generated during each
          stage of the probability binning process is stored. The
          matrices stored at the leaf nodes represent the binned events
          obtained after the stop criterion of minEvents has been
          achieved. These can be identified by the corresponding
          dataIndx fields provided by the rows in the table with the
          left or right column values of zero.  

 limits : A list containing the the boundaries of each hyperplane
          generated during probability binning

splitPars : A 'data.frame' containing two columns splitCol - indicates
          the column number of the 'flowFrame' , the split was
          performed.

          splitMed - The median value which was used as the threshold
          for splitting the 'flowFrame'

          The splitCol and splitMed parameters are utilized by the
          plotBins and shadeBins functions in visualizing the
          differences between control and test sample cases.

_A_u_t_h_o_r(_s):

     Nishant Gopalakrishnan

_S_e_e _A_l_s_o:

     'plotBins', 'binByRef'

_E_x_a_m_p_l_e_s:

     data(GvHD)
     res<-proBin(GvHD[[1]],200) 

