"FCSgate-class"           package:rflowcyt           R Documentation

_C_l_a_s_s "_F_C_S_g_a_t_e" _F_l_o_w _C_y_t_o_m_e_t_r_y _S_t_a_n_d_a_r_d _e_x_t_e_n_s_i_o_n _t_o _g_a_t_i_n_g

_D_e_s_c_r_i_p_t_i_o_n:

     This class of objects extends the class 'FCS-class' to incorporate
     information from gating which is a procedure by which rows or
     cells from the data are selected via one or two dimensional value
     restrictions or gating ranges.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("FCSgate", ...)'.
     Essentially this new object includes the 'FCS-class' object.

_S_l_o_t_s:

     '_g_a_t_e': Object of class '"matrix"' containing the gating indices
          such that each column corresponds to a different gating
          procedure/index and the rows correspond to the positions of
          the *original* row/cell observations. 

     '_h_i_s_t_o_r_y': Object of class '"vector"' containing the gating
          history strings such that each vector element corresponds to
          a different gating procedure/index and each string contains
          information about the particular gate, column variables that
          were used, and other additional comments.

     '_e_x_t_r_a_c_t_G_a_t_e_d_D_a_t_a._m_s_g': Object of class '"vector"' containing
          strings describing any extraction that took place
          corresponding to each gating procedure/index and history
          string; each string contains information about the particular
          corresponding gate column position and gate name and what
          value index was for inclusion/selection (ie, IndexValue.In)

     '_c_u_r_r_e_n_t._d_a_t_a._o_b_s': Object of class '"vector"' contains the
          current data positional values from the original data 

     '_d_a_t_a': Object of class '"matrix"' which holds integer data such
          that the columns are the variables (usually
          immunofluorescence measurements) and the rows are the cell
          observations. 

     '_m_e_t_a_d_a_t_a': Object of class '"FCSmetadata"' which holds
          information about the file, data, and column variables among
          other items in the header of the original raw FCS binary
          file. 

_E_x_t_e_n_d_s:

     Class '"FCS"', directly.

_M_e_t_h_o_d_s:

     No methods defined with class "FCSgate" in the signature.

_N_o_t_e:

     The methods 'createGate' and 'icreateGate', functionally without
     plots or interactively with plots, respectively, extends the
     'FCS-class' to the FCSgate-class.  Some interactive gating schemes
     are noted in 'FHCRC.HVTNFCS' and 'VRC.HVTNFCS'.  Further testing
     after gating is implemented by 'runflowcytests' on the particular
     variable of interest which is usually the Interferon Gamma
     Immunofluoroescence measurement.

_A_u_t_h_o_r(_s):

     A.J. Rossini, J.Y. Wan, and Zoe Moodie

_R_e_f_e_r_e_n_c_e_s:

     Trevor Hastie, Robert Tibshirani, and Jerome Friedman. The
     Elements of Statistical Learning: Data Mining, Inference, and
     Prediction. Springer Series in Statistics : New York, 2001.
     pp.279-283.

     Jerome H. Friedman and Nicholas I. Fisher. Bump Hunting in
     High-Dimensional Data. Tech Report. October 28, 1998.

     J. Paul Robinson, et al. Current Protocols in Cytometry.  John
     Wiley & Sons, Inc : 2001.

     Mario Roederer and Richard R. Hardy. Frequency Difference Gating:
     A Multivariate Method for Identifying Subsets that Differe between
     Samples. Cytometry, 45:56-64, 2001.

     Mario Roederer and Adam Treister and Wayne Moore and Leonore A.
     Herzenberg. Probability Binning Comparison: A Metric for
     Quantitating Univariate Distribution Differences. Cytometry,
     45:37-46, 2001.

     Keith A. Baggerly. Probability Binning and Testing Agreement
     between Multivariate Immunofluorescence Histograms: Extending the
     Chi-Squared Test. Cytometry, 45:141-150, 2001.

_S_e_e _A_l_s_o:

     'createGate', 'icreateGate', 'extractGatedData',
     'extractGateHistory', 'FHCRC.HVTNFCS', 'VRC.HVTNFCS',
     '"FCS-class"', 'runflowcytests'

_E_x_a_m_p_l_e_s:

     default.FCSgateobj<-new("FCSgate")

