relateChers              package:Ringo              R Documentation

_R_e_l_a_t_e _f_o_u_n_d _C_h_e_r_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 'cher's (ChIP-enriched regions) to
     annotated genomic features, such as transcripts.

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

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

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

      pl: Object of class 'cherList'

     gff: 'data.frame' holding genomic feature annotation

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

 verbose: logical; extended output to STDOUT?

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

     chers 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

     One can visualize such cher-feature relations as a graph using the
     Bioconductor package 'Rgraphviz'. See the script
     'graphChers2Transcripts.R' in Ringo's scripts directory for an
     example.

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

     An object of class 'cherList' with for each cher the elements
     'typeUpstream' and 'typeInside' 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 findChersOnSmoothed for an example

