aafTable-class            package:annaffy            R Documentation

_C_l_a_s_s _a_a_f_T_a_b_l_e, _a _t_a_b_u_l_a_r _m_i_c_r_o_a_r_r_a_y _d_a_t_a _c_l_a_s_s

_D_e_s_c_r_i_p_t_i_o_n:

     A class for storing and flexible output of microarray data to HTML
     and text formats.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects are generally created by any of the annotation table
     constructors that are also part of this package. Objects can also
     be created manually  by calls of the form 'new("aafList",
     probeids, table)'.

_S_l_o_t_s:

     '_p_r_o_b_e_i_d_s': Object of class 'character' containing the probe ids
          for each row of the table.

     '_t_a_b_l_e': Object of class 'list' containing 'aafList' objects all
          of the same length, representing the columns of the table.
          Each item in the list must have a unique name.

_M_e_t_h_o_d_s:

     _p_r_o_b_e_i_d_s (aafTable): Returns a character vector containing the
          probe ids for each row of the table.

     _p_r_o_b_e_i_d_s<- (aafTable): Sets the probe ids for the table rows. Can
          be set to 'character(0)' if unknown or not applicable.

     _c_o_l_n_a_m_e_s (aafTable): Returns a character vector containing the
          names of the columns stored in the table.

     _c_o_l_n_a_m_e_s<- (aafTable): Set the column names for the table. Each
          must be unique.

     _d_i_m (aafTable): Returns the dimensions of the table.

     _m_e_r_g_e (aafTable, aafTable, all = FALSE, all.x = all, all.y = all, 
          suffixes = c(".x",".y")): Merges two tables together,
          aligning common probe ids if possible. Duplicate column names
          are given suffixes to make them unique. Returns the merged
          table.

     _r_b_i_n_d (aafTable, aafTable, ...): Vertically combines tables by
          row. Requires that column names be identical and that all
          tables either have probe ids defined or not.

     [ Returns a subset of the table based on [row, column]. Indices
          may be passed as integers or probe ids/column names.

     [[ Returns the given table column. This also supports recursive
          subsetting to address columns, then cells, then sub-cells (if
          applicable). See Extract for more information.

     $ Returns the given table column.

     _s_a_v_e_H_T_M_L (aafTable, filename, title = "Bioconductor Affymetrix
          Probe Listing", colnames = colnames(aafTable), range =
          1:dim(aafTable)[1], open = FALSE, widget = FALSE):  Saves the
          table to HTML with the specified filename and title. Both the
          columns and the range of table rows can be specified. Range
          can either be specified as a character vector of probe ids or
          an integer vector of row positions. One can also specify
          whether to open the resulting file in the browser and whether
          to use a widget for column selection.

     _s_a_v_e_T_e_x_t (aafTable, filename, header = TRUE, colnames =
          colnames(aafTable), range = 1:dim(aafTable)[1], widget =
          FALSE): Saves the table to tab delimited text with specified
          filename and optional header.  Both the columns and the range
          of table rows can be specified.  Range can either be
          specified as a character vector of probe ids or an integer
          vector of row positions. One can also specify whether to use
          a widget for column selection.

_A_u_t_h_o_r(_s):

     Colin A. Smith, annaffy@colinsmith.org

_S_e_e _A_l_s_o:

     aafTable, aafTableFrame, aafTableAnn, aafTableInt