newCher                package:Ringo                R Documentation

_C_r_e_a_t_e _a _l_i_s_t _o_b_j_e_c_t _o_f _c_l_a_s_s _c_h_e_r

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

     This is just a simple convenience function to create a 'list' of
     class 'cher' (ChIP-enriched region).

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

     newCher(name, chr, start, end, cellType = NULL, antibody, maxLevel, score = NULL, probes = c(), ...)

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

    name: character; (if possible) unique identifier for the cher

     chr: character; chromosome the cher is located on

   start: integer; genomic start coordinate of the Cher

     end: integer; genomic end coordinate of the Cher

cellType: optional character describing the cell type in which the cher
          was identified.

antibody: required character vector describing the antibody or other
          characteristic for which fragments were supposedly enriched
          in immuno-precipitation step

maxLevel: numeric; maximal probe level in the cher

   score: optional numeric score of the cher

  probes: optional character vector of probe identifiers of probes that
          make up the cher

     ...: further arguments that will be additional elements of the
          'cher' list object

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

     a list object of class 'cher', see 'cher-class'

_N_o_t_e:

     this function is called by other Ringo functions, such as
     'findChersOnSmoothed' and normally need not be called by the user.

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

     Tammo Krueger, Joern Toedling

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

     'cher-class',  'findChersOnSmoothed'

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

       cher1 <- newCher("Suz12.Nudt2.upstream.cher",
                          chr="9", start=34318900, end=34320100,
                          antibody="Suz12",cellType="human",
                          maxLevel=2, score=99)
       print(cher1)

