cytoFrame-class            package:prada            R Documentation

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

     This class represents the data contained in a FCS 3.0 file or
     similar data structures.

_D_e_t_a_i_l_s:

     Although objects of class 'cytoFrame' can be used to hold
     arbitrary data of cell populations, the main focus lies on
     flow-cytometry data.

     FCS 3.0 is the Data File Standard for Flow Cytometry, Version
     FCS3.0. See the vignette of this package for additional
     information on using the object system for handling of
     flow-cytometry data.

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

     Objects can be created using
      '  new('cytoFrame,'
      '    exprs       = ...., # Object of class matrix'
      '    description = ....  # Object of class character'
      '  )'
      or the function 'readFCS'.

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


     '_e_x_p_r_s': Object of class 'matrix' containing the measured
          intensities. Rows correspond to cells, columns to the
          different channels. The 'colnames' attribute of the matrix is
          supposed to hold the names or identifiers for the channels.
          The 'rownames' attribute would usually not be set.

     '_d_e_s_c_r_i_p_t_i_o_n': A named character vector containing the experiment
          description as key-value pairs.

     '_w_e_l_l': A single integer vector giving the position of the well on
          a microtitre plate. This only applies when using the object
          within a 'cytoSet' collection and will usually be filled in
          by the function 'readCytoSet'.

     '_g_a_t_e': An object of class 'gateSet'. This object can be used to
          select defined subsets of the data, a process referred to as
          'gating' in the analysis of flow-cytometry data.

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


     [ subsetting. Returns an object of class 'cytoFrame'. The
          subsetting is applied to the 'exprs' slot, while the
          'description' slot is unchanged.

     _e_x_p_r_s, _e_x_p_r_s<- extract or replace the intensities.

     _d_e_s_c_r_i_p_t_i_o_n, _d_e_s_c_r_i_p_t_i_o_n<- extract or replace the description.

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

     _p_l_o_t scatterplot for 'cytoFrame' objects. The additional argument
          'gate' can be used to plot subsets of the data defined by
          either an object of class 'gate' or by a character vector
          giving the name of one of the gates in the list.

     _g_a_t_e,_g_a_t_e<- extract or replace the list of gates.

     _n_c_o_l,_n_r_o_w extract the dimensions of the data matrix.

     _a_p_p_e_n_d_G_a_t_e Append a gate or gateSet to the gate slot.

     _d_r_a_w_G_a_t_e Create an object of class 'gate' or 'gateSet' based on a
          selection made from the data. See 'gateMatrix' for further
          details.

     _h_i_s_t Draw a histogram of the data

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

     Florian Hahne, Wolfgang Huber

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

     'readFCS', 'cytoSet', 'gate', 'gateSet', 'gateMatrix'

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

     intens <- matrix(runif(100), ncol=4)
     colnames(intens) <- c("FL1-H", "FL2-H", "FL3-H", "FL4-H")

     a <- new("cytoFrame",
               exprs=intens,
               description=c(name="example data", date=date()))

     description(a)
     dim(exprs(a))           

     a[1:3, -4]

     plot(a)
     ## Not run: 
     g1 <- drawGate(a, name="Gate1")
     ## End(Not run)

