extractGateHistory         package:rflowcyt         R Documentation

_E_x_t_r_a_c_t_i_n_g _t_h_e _g_a_t_i_n_g _i_n_f_o_r_m_a_t_i_o_n _f_r_o_m _t_h_e _h_i_s_t_o_r_y

_D_e_s_c_r_i_p_t_i_o_n:

     The history string corresponding to a specific gating Index
     specified by 'gateNum' is retrieved and output as a list of
     specific components.

_U_s_a_g_e:

     extractGateHistory(x, gateNum)

_A_r_g_u_m_e_n_t_s:

       x: a "FCSgate" object created after using 'createGate'

 gateNum: the numeric column position of the gating index in the 'gate'
          matrix 

_V_a_l_u_e:

 gateNum: the numeric column position of the gating index in the 'gate'
          matrix

gateName: character name of the gating index specified in the 'gate'
          matrix

    type: type of gating (ie, "biscut", "uniscut", "bipcut", "bidcut")

biscut.quadrant: the quadrant specified (ie, ("+/+", "-/-", "+/-",
          "-/+"))

data.colpos: the gated parameter column positions in the 'data' matrix

data.colnames: the gated parameter column names in the 'data' matrix

IndexValue.In: the value of the index that specifies inclusion or
          selection

gatingrange: the vector of gating threshold(s)

prev.gateNum: the previous or most prior gating index column position
          in the 'gate' matrix

prev.gateName: the previous or most prior gating index column name in
          the 'gate' matrix

 comment: character string of the user-defined comment

_A_u_t_h_o_r(_s):

     A.J. Rossini and J.Y. Wan

_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:

     'FCS-class', 'FCSgate-class', 'createGate,
     \code{extractGatedData}'

_E_x_a_m_p_l_e_s:

      if (require(rfcdmin)) {
           data.there<-is.element("MC.053",objects())
           if ((sum(data.there) != length(data.there))) {
             ## obtaining the FCS objects from VRC data
             data(MC.053min)
           }
       
     ####  foo1 : Gating type: uniscut, univariate single cut
     foo1 <- createGate(MC.053, varpos=4, gatingrange=256,
                         type="uniscut", MY.DEBUG=TRUE)

     #### foo2.3 : Gating type : biscut -/-
     foo2.3 <- createGate(foo1, varpos=c(1,2),
                           gatingrange=c(256, 300),
                           type="biscut",
                           biscut.quadrant="-/-",
                           prev.gateNum=NULL,
                           MY.DEBUG=TRUE)

     ## obtain gate information for first uniscut gate
     gate.info1<-extractGateHistory(foo1, gateNum=1)

     ## obtain gate information for the second biscut gate
     gate.info2<-extractGateHistory(foo2.3, gateNum=2)

     ### foo2.3.1 : extraction
     foo2.3.1 <- extractGatedData(foo2.3, gateNum=2,
                                   IndexValue.In=1,
                                   MY.DEBUG=TRUE)
     ## obtain the second biscut gate information after
     ## subset/extraction of row observations
     gate.info2.1<-extractGateHistory(foo2.3.1, gateNum=2)
     }

