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 (_w_r_a_p_p_e_r _f_u_n_c_t_i_o_n)

_D_e_s_c_r_i_p_t_i_o_n:

     Wrapper around the 'segment' function for each strand of one or
     more chromosomes specified by the user. It does some typical
     preprocessing and I/O.

_U_s_a_g_e:

     segChrom(y, probeAnno, chr=1:17, strands=c("+", "-"), 
       nrBasesPerSegment = 1500, maxk = 3000, step = 7, confint = FALSE,
       confintLevel = 0.95, useLocks=TRUE, verbose=TRUE, savedir)

_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.

 strands: character scalar or vector specifying which strands to
          segment.

nrBasesPerSegment: integer (length 1): the parameter 'maxseg' of the
          'segment' function is calculated as the length of the
          chromosome divided by 'nrBasesPerSegment'. Thus, it
          determines the average segment length in the finest
          segmentation.

    maxk: passed on to  the function 'segment'.

    step: integer scalar, indicating the minimum distance between
          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.

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

useLocks: logical scalar. Should a file locking mechanism be used that
          allows for a simple-minded parallelization of this function.

 verbose: logical scalar. Should we be chatty about our progress?

 savedir: character scalar. If specified, resulting 'segmentation'
          objects are saved (with 'save') to this directory.

_D_e_t_a_i_l_s:

     This function is a wrapper for the 'segment' function. Refer to
     its help page for further details.

_V_a_l_u_e:

     An environment containing S4 objects of class '"segmentation"'
     called "1.+", "1.-", etc. (depending on the values in 'chr' and
     'strands'), where "+" and "-" indicate the strand and the
     preceding number refers to the chromosome. If 'savedir' is
     specified, there is also the side-effect that a series of files
     "1.+.rda", "1.-.rda", etc. is saved in that directory.

_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:

     ## Not run: 
       library("davidTiling")
       data("davidTiling")
       data("probeAnno")
       isDNA = seq(1:3)
       yn = normalizeByReference(davidTiling[,-isDNA],davidTiling[,isDNA], probeAnno=probeAnno)
       seg = segChrom(yn, probeAnno) ## this will take a while to run!
     ## End(Not run)

