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.

_U_s_a_g_e:

     ## S4 method for signature 'cytoFrame':
     exprs(object)
     \S4method{exprs<-}{cytoFrame,matrix}(object,value)
     ## S4 method for signature 'cytoFrame':
     description(object)
     \S4method{description<-}{cytoFrame,character}(object,value)
     ## S4 method for signature 'cytoFrame':
     colnames(object)
     \S4method{colnames<-}{cytoFrame,ANY}(object,value)
     ## S4 method for signature 'cytoFrame':
     show(object)
     \S4method{[}{cytoFrame,ANY}(x, i, j, ..., drop=FALSE)
     $.cytoFrame(x, val)

_A_r_g_u_m_e_n_t_s:

object,x: Objects of class 'cytoFrame'.

   value: Replacement value.

     i,j: Indices.

     ...: Further arguments that get passed on.

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

     FCS 3.0 is the Data File Standard for Flow Cytometry, Version
     FCS3.0.

_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.

_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.

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

     Wolfgang Huber

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

     'readFCS', 'cytoSet-class'

_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]

