MEDMEset-class             package:MEDME             R Documentation

_C_l_a_s_s "_M_E_D_M_E_s_e_t"

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

     This class is used in MEDME library to store MeDIP derived
     DNA-methylation estimates and to save further elaboration of
     these, in association with chromosomal and positional probe
     information

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("MEDMEset",
     ...)'. This object could initially host the MeDIP normalized
     logRatio data, as returned by the 'MEDME.readFiles' function.
     Afterwards, the same obejct is returned by most of the MEDME
     library function. Each time, a new slot is filled with additional
     data, as smoothed logR or Absolute/Relative Methylation Scores
     (AMS and RMS respectively). At the end of the analysis, usually
     after a call to the 'predict' function, the 'MEDME.writeFiles'
     function can be used to generate SGR or GFF files from this
     object.

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


     '_c_h_r': Object of class '"character"' : the probe-level chromosome
          asignments

     '_p_o_s': Object of class '"numeric"' : the probe-level genomic
          position

     '_l_o_g_R': Object of class '"matrix"' : the probe-level un-trasformed
          normalized MeDIP logRatios for each sample

     '_s_m_o_o_t_h_e_d': Object of class '"matrix"' : the probe-level smoothed
          MeDIP logRatios for each sample

     '_A_M_S': Object of class '"matrix"'  : the probe-level Absolute
          Methylation Score for each sample

     '_R_M_S': Object of class '"matrix"'  : the probe-level Relative
          Methylation Score for each sample

     '_C_G_c_o_u_n_t_s': Object of class '"numeric"'  : the probe-level count
          of CpGs

     '_o_r_g_a_n_i_s_m': Object of class '"character"' : the organism that the
          probe genomic positions are referring to, either hsa or mmu
          for homo sapiens or mus musculus respectively

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


     [ 'signature(x = "MEDMEset")': subsets the object based on its
          probes and/or samples

     _A_M_S 'signature(object = "MEDMEset")': extracts the Absolute
          Methylation Score from the AMS slot

     _C_G 'signature(object = "MEDMEset")': extracts the probe CpG count
          from the CGcounts slot

     _c_h_r 'signature(object = "MEDMEset")': extracts the probe
          chromosomal assignment

     _o_r_g 'signature(object = "MEDMEset")': extracts the organism

     _i_n_i_t_i_a_l_i_z_e 'signature(.Object = "MEDMEset")': automatically
          generates smoothed, AMS and RMS matrix when only the logR
          slot is filled

     _l_o_g_R 'signature(object = "MEDMEset")': extracts the matrix of
          MeDIP un-transformed logRatios 

     _p_o_s 'signature(object = "MEDMEset")': extracts the probe genomic
          position

     _R_M_S 'signature(object = "MEDMEset")': extracts the Relative
          Methylation Score from the RMS slot

     _s_h_o_w 'signature(object = "MEDMEset")': prints a summary of the
          object content

     _s_m_o_o_t_h_e_d 'signature(object = "MEDMEset")': extracts the Absolute
          Methylation Score from the AMS slot

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

     Mattia Pelizzola

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

     <URL:
     http://genome.cshlp.org/cgi/content/abstract/gr.080721.108v1>

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

     'MEDME.readFiles', 'MEDME.writeFiles'

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

     showClass("MEDMEset")

