plotAlongChrom2         package:tilingArray         R Documentation

_P_l_o_t _t_h_e _r_e_s_u_l_t_s _o_f _s_e_g_m_e_n_t_a_t_i_o_n _a_l_o_n_g _a _c_h_r_o_m_o_s_o_m_a_l _r_e_g_i_o_n

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

     Plot the results of segmentation along a chromosomal region

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

     plotAlongChrom2(chr, coord, highlight, segObj, y, probeAnno,
                            scoreShow = "pt", nrBasesPerSeg, gff,
                            haveLegend=TRUE)

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

     chr: integer of length 1 with the number of the chromosome for
          which to make the plot.

   coord: integer of length 2 with start and end coordinates of the
          plot.

highlight: optional, list with two elements: a single numeric value
          'coord' and a character 'strand'. If present, this position
          is marked by a vertical red bar on the coordinate axis.

  segObj: environment containing three types of data: 1. microarray
          intensities in along-chromosome order, 2. segmentation
          (output of findSegments), 3. segment score (dataframe, can be
          missing iff 'nrBasesPerSeg' is present), 4. the threshold for
          "transcribed" segments. See also Paragraph _Intensities_ in
          the _Details_ section. This is currently simply an
          environment that is expected to contain certain objects with
          certain names. In future version, this is supposed to be
          replaced by a proper S4 object.

       y: numeric vector of intensities from a (virtual) array, see
          Paragraph _Intensities_ in the _Details_ section.

probeAnno: environment with probe annotations, see details.

scoreShow: character, name of a column in 'segScore' that is to be used
          for the coloring of the segments.

nrBasesPerSeg: numeric of length 1 with the average number of
          nucleotide bases per segment. Can be missing iff 'segScore'
          is present.

     gff: data frame with genome annotation from the GFF file.

haveLegend: logical, should the plot contain a legend?

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

     _Intensities_: There are two alternative, mutually exclusive ways
     of providing the intensities to be plotted to this function.

        1.  Via the parameters 'y' and 'probeAnno'. Then, 'y' is a
           vector of intensities, and 'probeAnno' is an environment
           that contains integer vectors with start positions along the
           chromosomes and indices in 'y' of the probes. For example,
           the start positions and indices of probes for the + strand
           of chromosome 1 would be described by environment elements
           '"1.+.start"' and '"1.+.index"', respectively.

        2.  Via the parameter 'segRes'. In that case, the intended
           workflow for using this function is as follows: First, use
           the script 'segment.R' to generate a segmentation. This can
           be run in parallel on several processors, separately for
           each chromosome and strand. The results of this are stored
           in files of the name '1.+.rda', '1.-.rda', '2.+.rda', and so
           forth, typically within a dedicated directory. Then, the
           script 'viewsegmentation.R' can be used to view the
           segmentation results. It collects the 'R' objects in these
           '.rda' files into the environment 'segRes', with which it
           calls  this function.

           Furthermore, the script 'scoreSegments.R' can be used to
           calculate scores for each segment, which can be passed to
           this function using the 'segRes' argument.

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

     Wolfgang Huber <huber@ebi.ac.uk>

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

       ## 
      

