makePDpackage       package:makePlatformDesign       R Documentation

_P_l_a_t_f_o_r_m _D_e_s_i_g_n _P_a_c_k_a_g_e _M_a_k_e_r

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

     This function creates the Platform Design package for Affymetrix
     and NimbleGen chips.

     The objects generated by this package are soon going to be created
     by the 'pdInfoBuilder' package.

     For Affymetrix SNP arrays, use the 'pdInfoBuilder' package.

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

     makePDpackage(designFile, file1 = NULL, file2 = NULL,
                   manufacturer = c("affymetrix", "nimblegen"),
                   type = c("expression", "SNP", "tiling", "exon"),
                   extra = NULL, genomebuild = "hg12")

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

designFile: a string with the name of the CDF/NDF file

   file1: the FASTA/tab sequence file or the XYS file

   file2: the annotation or *.POS file

manufacturer: a choice between "affymetrix" or "nimblegen"

    type: array type: "expression", "SNP", "tiling" or "exon"

   extra: a list with several options for customization

genomebuild: genome build information

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

     'designFile' is either a CDF or an NDF file, depending on the
     platform being used.

     'file1' is the FASTA sequence file if using an Affymetrix SNP
     Chip. It will be the tab-delimited sequence file if using an
     Affymetrix Expression Chip. If using a NimbleGen Chip, then it is
     an XYS file.

     'file2' is the annotation file for Affymetrix Chips or the *.POS
     file for NimbleGen Chips. Required for SNP Chips, optional
     otherwise.

     'extra' is a list containing *all* the following elements:
     "packagename" (desired package name), "cdf.path" (path to the
     CDF), "package.path" (path where the package is to be saved),
     "author" (author of the package), "maintainer" (maintainer of the
     package), "version" (version of the package), "unlink" (boolean,
     deletes the package.path dir if it already exists), "verbose"
     (boolean).

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

     Either an 'affysnpBatch' or an 'affyexprsBatch' object, depending
     on the type of the array (SNP or expression).

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

     Benilton Carvalho bcarvalh@jhsph.edu

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

     'writePackage'

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

     ## NOT RUN
     ##
     ## -- Affymetrix Expression Chip --
     ## makePDpackage("CDF", "TAB-sequence-file", manufacturer="affymetrix",
     ##                type="expression")
     ##
     ## -- Affymetrix SNP Chip --
     ## makePDpackage("CDF", "FASTA", "ANNOT", manufacturer="affymetrix",
     ##                type="SNP")
     ##
     ## -- NimbleGen Expression Chip --
     ## makePDpackage("NDF", "XYS", "POS", manufacturer="nimblegen",
     ##                type="expression")

