relatePeaks              package:Ringo              R Documentation

_R_e_l_a_t_e _f_o_u_n_d _p_e_a_k_s _t_o _g_e_n_o_m_i_c _f_e_a_t_u_r_e_s

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

     This function relates found peaks to annotated genomic features,
     such as transcripts.

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

     relatePeaks(pl, gff, upstream = 5000, verbose = TRUE)

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

      pl: Object of class 'peakList'

     gff: 'data.frame' holding genomic feature annotation

upstream: up to how many bases upstream of annated genomic features
          should peaks be counted as related to that feature (see
          details)

 verbose: logical; extended output to STDOUT?

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

     Peaks will be counted as related to genomic features, if

        *  their middle position is located between start and end
           position of the feature

        *  their middle position is located not more than argument
           'upstream' bases upstream of the feature start

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

     An object of class 'peakList' with for each peak the elements
     'typeUpstream' and 'typeDownstream' filled in with the names of
     the features that have been related to.

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

     Joern Toedling toedling@ebi.ac.uk

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

       # see findPeaksOnSmoothed for an example

