scoreSegments          package:davidTiling          R Documentation

_S_c_o_r_e _s_e_g_m_e_n_t_s

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

     Score the segments found by a previous call to findSegments by
     comparing to genome annotation

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

     scoreSegments(s, gff, 
       nrBasePerSeg = 1500, 
       probeLength  = 25,
       params = c(overlapFraction = 0.5, oppositeWindow = 100, flankProbes=10),
       verbose = TRUE)

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

       s: environment. See details.

     gff: GFF dataframe.

nrBasePerSeg: Numeric of length 1. This parameter determines the number
          of segments.

probeLength: Numeric of length 1.

  params: vector of additional parameters, see details.

 verbose: Logical.

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

     This function scores segments. It is typically called after a
     _segmentation_. For an example segmentation script, see the script
     'segment.R' in the 'scripts' directory of this package. For an
     example scoring script, which loads the data and then calls this
     function, see the script 'scoreSegments.R'.

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

     A dataframe with columns as described in the details section.

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

     W. Huber <huber@ebi.ac.uk>

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

