copynumberConversion      package:beadarraySNP      R Documentation

_C_o_n_v_e_r_s_i_o_n _t_o _C_o_p_y_n_u_m_b_e_r _a_n_a_l_y_s_i_s _o_b_j_e_c_t_s

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

     SnpSetIllumina objects are converted to other objects for
     numerical analysis

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

       convert2aCGH(object,normalizedTo=2,organism="hsa")
       convert2SegList(object,normalizedTo=2,organism="hsa")

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

  object: SnpSetIllumina object

normalizedTo: numeric, 'normal' copynumber datavalue for object

organism: character, organism used in object. Currently 'hsa' and 'mmu'
          are recognized. Used to convert sex chromosomes to their 
          proper numerical representation

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

     These functions produce objects that can be used by the analysis
     functions in the aCGH or snapCGH packages. The SnpSetIllumina
     intensity values are stored in a linear scale. Both types of
     objects assume a logarithmic scale, so the values are transformed
     to a log2 scale  centered around 0.

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

     'convert2aCGH' returns a 'aCGH' object as used in the aCGH
     package. 'convert2SegList' returns a 'SegList' object as used in
     the snapCGH package.

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

     Jan Oosting

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

     'SnpSetIllumina-class', 'aCGH-class', 'SegList-class'

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

