CGHregions            package:CGHregions            R Documentation

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

     Dimension Reduction for Array CGH Data with Minimal Information
     Loss

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

             CGHregions(input, averror=0.01)

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

   input: An object of class 'cghCall', a character string or a
          dataframe. See details for information on the latter two.

 averror: Maximal information loss allowed. 

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

     Please read the article and the supplementary information for
     detailed information on the algorithm.

     If the input is not an object of class 'cghCall' it should be
     either a dataframe or a tabseparated textfile (textfiles must
     contain a header). The first three columns should contain the
     name, chromosome and position in bp for each array target
     respectively. The chromosome and position column must contain
     numbers only. Following these is a column with log2 ratios for
     each of your samples. If the input type is a textfile, missing
     values should be represented as 'NA' or an empty field.

     The algorithm reduces the call matrix to a smaller matrix that
     contains regions rather than individual clones.  The regions
     consist of consequtive clones the signatures of which are very
     much alike. The dimension reduction  is potentially for testing
     and clustering puposes. The amount of information lost by this
     dimension  reduction is controlled by 'averror'. The larger
     'averror', the less regions will result.

_V_a_l_u_e:

     This function returns an object of class 'cghRegions'

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

     Mark van de Wiel and Sjoerd Vosse Maintainer: Mark van de Wiel
     <mark.vdwiel@vumc.nl>

_R_e_f_e_r_e_n_c_e_s:

     Mark A. van de Wiel and Wessel N. van Wieringen (2007).
     CGHregions: Dimension Reduction for Array CGH Data with Minimal
     Information Loss. _Cancer Informatics, 2_, 55-63.

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

             data(WiltingCalled)
             result <- CGHregions(WiltingCalled)

