qb.sweave               package:qtlbim               R Documentation

_R_u_n _s_w_e_a_v_e _t_o _a_u_t_o_m_a_t_e _Q_T_L _s_e_a_r_c_h _w_i_t_h _M_C_M_C _s_a_m_p_l_e_s.

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

     This routine runs a separate Sweave file (*.Rnw) of commands,
     making substitutions for the user-supplied data and thresholds. It
     can be used to automate the search for genetic architecture.

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

     qb.sweave(cross, pheno.col = 1, n.iter = 3000, n.draws = 64,
       scan.type = "2logBF", hpd.level = 0.5,
       upper.threshold, SweaveFile, SweaveExtra, PDFDir, remove.qb = TRUE)

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

   cross: Object of class 'cross'.

pheno.col: Phenotype column in object 'cross'.

  n.iter: Number of MCMC iterations to be stored.

 n.draws: Number of MC draws to use for 'fitqtl'.

scan.type: Type of 1-D and 2-D scan to perform; see 'qb.scanone'.

hpd.level: Highest probability density level for scan; see 'qb.hpdone'.

upper.threshold: Threshold for upper triangle (epistasis) in 2-D scan;
          see 'qb.scantwo'.

SweaveFile: Name of 'Sweave' file (default is 'system.file("doc",
          "hyperslide.Rnw", package = "qtlbim")').

SweaveExtra: Name of user-supplied extra 'Sweave' file (default is
          'NULL').

  PDFDir: Name of directory to store PDF files (default is 'phenoPDF',
          where 'pheno' is the name associated with phenotype
          'pheno.col').

remove.qb: Remove constucted objects if 'TRUE'.

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

     This is a simple shell around the 'Sweave' routine to create
     customized documents with embedded QTL analysis. The default file
     'system.file("doc", "hyperslide.Rnw", package = "qtlbim")' creates
     a "beamer" style PDF slide show. An alternative file
     'system.file("doc", "hyperpaper.Rnw", package = "qtlbim")' creates
     a preprint document. Both require post-processing with 'pdflatex'.

     A user-defined section can be added to the automated documents,
     using the 'SweaveExtra' option. We have provided
     'system.file("external", "hyperslideextra.Rnw", package =
     "qtlbim")' for the slide version and 'system.file("external",
     "hyperpaperextra.Rnw", package = "qtlbim")' for the preprint
     version.

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

     Brian S. Yandell, yandell@stat.wisc.edu

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.qtlbim.org>

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

     'Sweave'

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

     ## Not run: 
     data(hyper)

     ## Create default slide show LaTeX source without extra section.
     qb.sweave(hyper)

     ## Turn LaTeX into PDF. Run twice to get outline correct.
     ## Need pdflatex on your system.
     system("pdflatex hyperslide")
     system("pdflatex hyperslide")

     ## Create document form, with extra section.
     qb.sweave(hyper,
       SweaveFile = system.file("external", "hyperpaper.Rnw", package = "qtlbim"))
       SweaveExtra = system.file("external", "hyperpaperextra.Rnw",
         package = "qtlbim"))
     system("pdflatex hyperpaper")
     system("pdflatex hyperpaper")
     ## End(Not run)

