plot.peak               package:Ringo               R Documentation

_P_l_o_t _i_d_e_n_t_i_f_i_e_d _p_e_a_k_s

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

     Function for plotting identified peaks

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

     ## S3 method for class 'peak':
     plot(x, dat, probeAnno, samples=NULL, extent = 1000, gff = NULL, ...)

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

       x: object of class 'peak'

     dat: data object of class 'ExpressionSet' that was used for
          function 'findPeaksOnSmooth'

probeAnno: environment holding probe to genome mappings

 samples: which samples to plot, either a numeric vector of entries in
          1 to 'ncol(dat)', or character vector with entries in
          'sampleNames(dat)' or 'NULL' meaning plot the levels from all
          samples in the ExpressionSet

  extent: integer; how many base pairs to the left and right should the
          plotted genomic region be extended

     gff: data frame with gene/transcript annotation

     ...: further arguments passed on to function 'chipAlongChrom'

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

     called for generating the plot; 'invisible(NULL)'

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

     Joern Toedling

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

     'chipAlongChrom'

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

      ## Not run: 
       plot(p, smoothX, probeAnno=exProbeAnno, gff=exGFF)
      
     ## End(Not run)

