CGcount                package:MEDME                R Documentation

_D_e_t_e_r_m_i_n_i_n_g _t_h_e _c_o_u_n_t _o_f _C_p_G _d_i_n_u_c_l_e_o_t_i_d_e_s _f_o_r _a _s_e_t _o_f _g_e_n_o_m_i_c _l_o_c_a_t_i_o_n_s

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

     The count of CpGs is determined in each window of size wsize, with
     or withouth weighting, for each probe according to its position,
     chromosome and genome realease

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

     CGcount(data, wsize = 1000, wFunction = "linear")

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

    data: An object of class MEDMEset

   wsize: number; the size of the smoothing window, in bp 

wFunction: string; the type of weighting function, to choose among
          linear, exp, log or none 

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

     Only human and mouse are currently supported. The respective
     genomic sequence metadata library needs to be downloaded from the
     Bioconductor website, installed and loaded (around 800Mb). Please
     note that only the last genome release should be used. LiftOver
     UCSC tool could be used for batch conversion of old genomic
     position to the last genome release.

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

     An object of class MEDMEset is returned where the count of CpGs
     for each probe has been saved on the CGcount slot.

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

     'smooth'

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

     data(testMEDMEset)
     ## just an example with the first 1000 probes
     testMEDMEset = smooth(data = testMEDMEset[1:1000,])
     library(BSgenome.Hsapiens.UCSC.hg18)
     testMEDMEset = CGcount(data = testMEDMEset)

