import.genome.scheme           package:xps           R Documentation

_I_m_p_o_r_t _C_L_F, _P_G_F _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 CLF, PGF and transcript annotation files
     into a ROOT file and create S4 class SchemeTreeSet

_U_s_a_g_e:

     import.genome.scheme(filename   = character(0),
                          filedir    = getwd(),
                          layoutfile = character(0),
                          schemefile = character(0),
                          transcript = character(0),
                          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.

layoutfile: name of CLF-file, including full path.

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

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

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.genome.scheme' is used to import all information for an
     Affymetrix whole genome array into a 'ROOT' scheme file, including
     CLF and PGF-files, and the   current Afymetrix  transcript
     annotation files. 

     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  new
     annotation files are 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.

_W_a_r_n_i_n_g:

     The current version of 'xps' is able to import all Affymetrix
     genome array annotation files up to November 2008, i.e. all files
     of release 3 (r3) and earlier. However, in January 2009 Affymetrix
     has updated all CLF, PGF and annotation files to release 4 (r4)
     and added a new probeset annotation file, thus in effect changing
     the whole genome arrays to exon arrays!

     Thus, for release 4 (r4) files, function 'import.genome.scheme'
     can no longer be used, but you must use function
     'import.exon.scheme' instead (see examples).

_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.HuGene10stv1.na27"' but use
     'filename="Scheme_HuGene10stv1_na27"' instead. Extension "root" is
     added automatically, so that ROOT is able to recognize the file as
     ROOT file.

     Do not set 'add.mask=TRUE' unless you know that your computer has
     sufficient RAM.

     Do not add item 'control' unless you want to use one of the old
     annotation files where the probeset annotation file does not
     contain the AFFX controls.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     'import.exon.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 HuGene-1_0-st-v1 whole genome array
     scheme.hugene10stv1r3.na27 <- import.genome.scheme("Scheme_HuEx10stv1r3_na27",filedir=scmdir,
                                   layoutfile=paste(libdir,"HuGene-1_0-st-v1.r3.analysis_libraryfile/HuGene-1_0-st-v1.r3.clf",sep="/"),
                                   schemefile=paste(libdir,"HuGene-1_0-st-v1.r3.analysis_libraryfile/HuGene-1_0-st-v1.r3.pgf",sep="/"),
                                   transcript=paste(anndir,"HuGene-1_0-st-v1.na27.hg18.transcript.csv",sep="/"))

     ## access ROOT scheme file from new R session
     scheme.hugene10stv1r3 <- root.scheme(paste(scmdir,"Scheme_HuEx10stv1r3_na27.root",sep="/"))
     ## End(Not run)

