newPeak                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 _p_e_a_k

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

     This is just a simple convenience function to create a 'list' of
     class 'peak'.

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

     newPeak(name, chr, start, end, cellType = NULL, modification, maxPeak, score = NULL, probes = c(), ...)

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

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

     chr: character; chromosome the peak is located on

   start: integer; genomic start coordinate of the peak

     end: integer; genomic end coordinate of the peak

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

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

 maxPeak: numeric; maximal probe level in teh peak

   score: optional numeric score of the peak

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

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

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

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

_N_o_t_e:

     this function is called by other Ringo functions, such as
     'findPeaksOnSmoothed' 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:

     'peak-class',  'findPeaksOnSmoothed'

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

       my.peak <- newPeak("H3ac.HAND2.upstream.peak",
                          chr="8", start=60210400, end=60213000,
                          modification="H3ac",cellType="cellLine.HL1",
                          maxPeak=3.5, score=100)
       print(my.peak)

