gateSet-class             package:prada             R Documentation

'_g_a_t_e_S_e_t': _a _c_l_a_s_s _f_o_r _s_u_b_s_e_t_t_i_n_g _f_l_o_w-_c_y_t_o_m_e_t_r_y _d_a_t_a _b_y _d_e_f_i_n_i_n_g
_m_u_l_t_i_p_l_e _r_e_g_i_o_n_s _i_n _t_w_o-_d_i_m_e_s_i_o_n_a_l _p_r_o_j_e_c_t_i_o_n_s _o_f _t_h_e _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     In flow-cytometry analysis, regions in two-dimensional projections
     of the data space often have to be selected. Objects of this class
     can store the properties for several of these selections

_C_r_e_a_t_i_n_g _O_b_j_e_c_t_s:

     Objects can be created using methods of the generic function 
     'drawGate' or via
      '  new("gateSet",'
      '    glist = ....,   # object of class list'
      '  )'

_S_l_o_t_s:


     '_n_a_m_e': Object of class 'character' giving the name of the object.
          You can reference the object by its name for subsequent
          operations (e.g. plotting).

     '_g_l_i_s_t': Object of class '"list"' with items of class 'gate'. The
          individual 'gate' objects will be combined according to the
          value of their slot 'logic'.

_M_e_t_h_o_d_s:


     _a_p_p_l_y_G_a_t_e: 'applyGate(x, data)'
          applies the gating of object 'x' on data objects of class
          'cytoFrame' or 'matrix'

     _l_e_n_g_t_h length of slot 'glist'

     _s_h_o_w 'display summary'

     _n_a_m_e_s, _n_a_m_e_s<- extract or replace the names of the individual
          'gate' objects.

     [ subset to 'gateSet' objects.

     [[ subset to individual 'gate' objects.   

     _a_p_p_e_n_d_G_a_t_e_s append a 'gate' or 'gateSet' to a 'cytoFrame'

_A_u_t_h_o_r(_s):

     Florian Hahne

_S_e_e _A_l_s_o:

     'cytoFrame', 'gateMatrix', 'gate'

_E_x_a_m_p_l_e_s:

     sampdat <- readFCS(system.file("extdata", "fas-Bcl2-plate323-04-04.A01",
                                    package="prada"))
     g1 <- new("gate", name="G1", gateFun=function(x)x[,"FSC-H"]<500, logic="&",
               colnames="FSC-H")
     g2 <- new("gate", name="G2", gateFun=function(x)x[,"SSC-H"]>800, logic="&",
               colnames="SSC-H")
     g3 <- new("gate", name="G3", gateFun=function(x)x[,"FL1-H"]>800, logic="&",
               colnames="FL1-H")
     gs <- new("gateSet", name="Set1", glist=list(G1=g1, G2=g2))
     length(gs)
     gs[[1]]
     gs[1]
     gsnames <- names(gs)
     names(gs) <- gsnames
     applyGate(sampdat, gs)
     applyGate(exprs(sampdat), gs)
     gate(sampdat) <- gs
     applyGate(sampdat, 1)
     applyGate(sampdat, "G1")
     applyGate(sampdat, TRUE)
     appendGates(sampdat, g3)

