segChrom             package:tilingArray             R Documentation

_F_i_t _a _p_i_e_c_e_w_i_s_e _c_o_n_s_t_a_n_t _c_u_r_v_e _t_o _a_l_o_n_g _c_h_r_o_m_o_s_o_m_e _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     This function calls the 'segment' function for each strand of one
     or more chromosomes specified by the user.

_U_s_a_g_e:

     segChrom(y, probeAnno, chr=1, nsegs, nrBasesPerSegment = 1500, 
                  step=7, confint=FALSE, confintLevel=0.95, save=FALSE, savedir=NULL)

_A_r_g_u_m_e_n_t_s:

       y: ExpressionSet or matrix containing the data to be segmented.

probeAnno: environment with probe annotations. See package
          'davidTiling' for an example (?probeAnno).

     chr: integer scalar or vector specifying which chromosome(s) to
          segment.

   nsegs: integer vector specifying the maximum number of segments (= 1
          + maximum number of change points) for each chromosome and
          strand.  If missing, this value is calculated by dividing the
          number of bases on a chromosome by 'nrBasesPerSegment'.

nrBasesPerSegment: integer (length 1): maximum length of a segment.

    step: integer, indicating the minimum distance between the
          consecutive probes. In cases when probes are offset by less
          than 'step' bases, the probes are sampled to achieve the
          desired spacing.

 confint: logical scalar.  If 'TRUE', confidence intervals for each
          change-point are calculated.  Otherwise ('FALSE'), no
          confidence intervals are returned.

confintLevel: numeric scalar between 0 and 1 indicating the probability
          level for the confidence intervals calculated for each
          change-point.

    save: logical scalar. If 'TRUE' the results of each segmentation
          are saved to file in the 'savedir' directory. If 'FALSE'
          (default), the results are not saved to file.

 savedir: optional character string specifying the filepath where the
          segmentation results will be saved. Only used when
          'save=TRUE'. Defaults to current working directory.

_D_e_t_a_i_l_s:

     This function is a wrapper for the 'segment' function which fits
     piecewise constant curves to along chromosome data. It calls
     'segment' for each strand of the chromosomes specified by the
     'chr' argument. Refer to the 'segment' help page for further
     details.

_V_a_l_u_e:

     An environment with containing S4 objects of class
     '"segmentation"' called "1.+", "1.-", etc (depending on 'chr'),
     where "+" and "-" indicates the strand and the preceding number
     refers to the chromosome number. If 'save=TRUE', a series of
     files, "1.+.rda", "1.-.rda", etc (depending on 'chr') are saved in
     the directory specified.

_A_u_t_h_o_r(_s):

     Matt Ritchie <ritchie@ebi.ac.uk> and Wolfgang Huber
     <huber@ebi.ac.uk>

_E_x_a_m_p_l_e_s:

     ## library("davidTiling")
     ## data("davidTiling")
     ## data("probeAnno")
     ## isDNA = seq(1:3)
     ## yn = normalizeByReference(davidTiling[,-isDNA],davidTiling[,isDNA], probeAnno=probeAnno)
     ## seg1 = segChrom(yn, probeAnno, chr=1) # this will take a while to run!

