import.expr.scheme            package:xps            R Documentation

_I_m_p_o_r_t _C_D_F, _p_r_o_b_e _a_n_d _a_n_n_o_t_a_t_i_o_n _f_i_l_e_s _i_n_t_o _a _S_c_h_e_m_e_T_r_e_e_S_e_t

_D_e_s_c_r_i_p_t_i_o_n:

     Import the Affymetrix CDF, probe and annotation files into a ROOT
     file and create S4 class SchemeTreeSet

_U_s_a_g_e:

     import.expr.scheme(filename   = character(0),
                        filedir    = getwd(),
                        schemefile = character(0),
                        probefile  = character(0),
                        annotfile  = character(0),
                        chipname   = NULL,
                        add.mask   = FALSE,
                        verbose    = TRUE)

_A_r_g_u_m_e_n_t_s:

filename: file name of ROOT scheme file.

 filedir: system directory where ROOT scheme file should be stored.

schemefile: name of CDF-file, including full path.

probefile: name of probe-file, including full path.

annotfile: name of annotation-file, including full path.

chipname: optional chip name when using an alternative CDF-file.

add.mask: logical. If 'TRUE' mask information will be included as slot
          'mask'.

 verbose: logical, if 'TRUE' print status information.

_D_e_t_a_i_l_s:

     'import.expr.scheme' is used to import all information for an
     Affymetrix  expression array into a 'ROOT' scheme file, including
     CDF-file, the corresponding probe file, and the current Afymetrix
     annotation file. 

     Usually, 'chipname' is extracted from the name of the CDF-file,
     however, when using an alternative CDF-file, e.g. from BrainArray
     or AffyProbeMiner, a 'chipname' must be supplied which starts with
     (or contains) the exact Affymetrix chip name.

     An S4 class 'SchemeTreeSet' will be created, serving as R wrapper
     to the  'ROOT' scheme file 'filename'.

     Since a new 'ROOT' scheme file needs only to be created when a new
     annotation file is available from the Affymetrix website, it is
     recommended to store all 'ROOT' scheme files in a commonly
     accessible system directory 'filedir'.

     Use function 'root.scheme' to access the 'ROOT' scheme file from
     new R sessions to avoid creating a new 'ROOT' scheme file for
     every session.

_V_a_l_u_e:

     A 'SchemeTreeSet' object.

_N_o_t_e:

     As mentioned above, use function 'root.scheme' to access the 
     'ROOT' scheme file from new R sessions to avoid creating a new
     'ROOT'  scheme file for every R session.

     Do not separate 'filename' of ROOT files with dots, use
     underscores, e.g. do not use  'filename="Scheme.Test3.na27"' but
     use 'filename="Scheme_Test3_na27"' or simply
     'filename="SchemeTest3na27"' instead. Extension "root" is added
     automatically, so that ROOT is able to recognize the file as ROOT
     file.

     For a few probesets, parsing the Affymetrix annotation files will
     provide ambiguous results. Setting 'verbose=11' will list these
     probesets.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     'import.exon.scheme', 'import.genome.scheme', 'root.scheme',
     'SchemeTreeSet'

_E_x_a_m_p_l_e_s:

     ## Not run: 
     ## define paths
     scmdir <- "/common/path/schemes"
     libdir <- "/my/path/Affy/libraryfiles"
     anndir <- "/my/path/Affy/Annotation"

     ## create scheme for Test3 GeneChip
     scheme.test3.na27 <- import.expr.scheme("Scheme_Test3_na27",filedir=scmdir,
                          schemefile=paste(libdir,"Test3.CDF",sep="/"),
                          probefile=paste(libdir,"Test3_probe.tab",sep="/"),
                          annotfile=paste(anndir,"Test3.na27.annot.csv",sep="/"))

     ## access ROOT scheme file from new R session
     scheme.test3 <- root.scheme(paste(scmdir,"Scheme_Test3_na27.root",sep="/"))

     ## create scheme for HG-U133_Plus_2 GeneChip
     scheme.hgu133p2.na27 <- import.expr.scheme("Scheme_HGU133p2_na27",filedir=scmdir,
                             schemefile=paste(libdir,"HG-U133_Plus_2.cdf",sep="/"),
                             probefile=paste(libdir,"HG-U133-PLUS_probe.tab",sep="/"),
                             annotfile=paste(anndir,"HG-U133_Plus_2.na27.annot.csv",sep="/"))
     ## access ROOT scheme file from new R session
     scheme.hgu133p2 <- root.scheme(paste(scmdir,"Scheme_HGU133p2_na27.root",sep="/"))
     ## End(Not run)

