html              package:GeneticsBase              R Documentation

_G_e_n_e_r_a_t_e _s_u_m_m_a_r_y _t_a_b_l_e _f_i_l_e_s _f_o_r _g_e_n_o_t_y_p_e _o_b_j_e_c_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Generate summary table files for genotype objects

_U_s_a_g_e:

     #### HTML file format
     html
     ## S3 method for class 'LD':
     html(x, filename = "", digits = 3, ...)
     ## S3 method for class 'GeneticsBaseSummary':
     html(x, filename = "", ...)
     ## S3 method for class 'markerSummary':
     html(x, filename = "", plot.format = "pdf", 
                        sep=".", verbose=TRUE, ...)

     #### plain text file format
     txt
     ## Default S3 method:
     txt(x, filename="", eol="\n", ...)
     ## S3 method for class 'markerSummary':
     txt(x, filename = "", plot.format = "pdf",
                        sep=".", verbose=TRUE, ...)

     #### LaTex file format
     latex
     ## Default S3 method:
     latex(x, filename="", ...)
     ## S3 method for class 'LD':
     latex(x, filename = "", digits = 3, ...)
     ## S3 method for class 'GeneticsBaseSummary':
     latex(x, filename = "", ...)
     ## S3 method for class 'markerSummary':
     latex(x, filename = "", plot.format = "pdf",
                        sep=".", verbose=TRUE, ...)

_A_r_g_u_m_e_n_t_s:

       x: Object to be rendered to html/txt/latex

filename: Output filename, see below for details.

     eol: End of line marker, defaults to '"\n"'. MS-DOS/MS-Windows
          uses '"\r\n"' 

  digits: Number of digits to display

plot.format: Graphics format for LD plot. Only '"pdf"' is currently
          supported

     sep: Separatior used to join the file prefix provided by
          'filename' and descriptive text when generating file names

 verbose: Show names of created files.

     ...: Additional parameters to pass to component methods

_D_e_t_a_i_l_s:

     For 'alleleSummary', 'genotypeSummary', and 'LD' objects, the
     'filename' argument is either the exact name of the file to be
     created, or "" which will print the output to the console.

     For 'markerSummary' objects, 'filename' may be either '""' or a
     prefix used to create file names. If 'filename=""' all output is
     printed to the R console.  Otherwise, filenames for each component
     are constructed by combining the prefix specified by 'filename',
     the separator specified by 'sep', a string descibing the file
     contents (one of "alleleSummary", "genotypeSummary", and "LD"),
     and the file extension ".html".

_V_a_l_u_e:

     Nothing of interest

_A_u_t_h_o_r(_s):

     Nitin Jain nitin_jain@pfizer.com and Gregory R. Warnes
     warnes@bst.rochester.edu

_S_e_e _A_l_s_o:

     'alleleSummary', 'genotypeSummary', 'markerSummary', 'LD'

_E_x_a_m_p_l_e_s:

     data(CAMP)

     ###
     # Generate a plain text allele summary table
     ###
     aS <- alleleSummary(CAMP)
     # display inline
     txt(aS, filename="")
     # create CAMP_alleleSummary.txt
     txt(aS, filename="CAMP.alleleSummary.html") 

     ###
     # Generate an HTML genotype summary table
     ###
     gS <- genotypeSummary(CAMP)
     # display inline
     html(gS, filename="")
     # create CAMP_genotypeSummary.html
     html(gS, filename="CAMP.genotypeSummary.html")

     ###
     # Generate a LaTeX Linkage Disequilibrium table
     ###
     ld <- LD(CAMP)
     # display inline
     latex(ld, filename="")
     # create CAMP_LDSummary.html
     latex(ld, filename="CAMP.LD.html")

     ###
     # Generate a complete set of summary tables 
     ###
     mS <- markerSummary(CAMP)
     # Plain text format
     txt(mS, filename="CAMP", sep="_")
     # HTML format
     html(mS, filename="CAMP", sep="_")
     # LaTeX format
     latex(mS, filename="CAMP", sep="_")

