preprocessedLoader           package:macat           R Documentation

_R_e_a_d _i_n _d_a_t_a _a_n_d _p_r_o_d_u_c_e _M_A_C_A_T _l_i_s_t

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

     This function reads expression data either from a saved R-file
     (.RData,.rda), or from a tab-separated text-file (.xls). For
     building a MACAT-list structure from objects in your workspace,
     you can either use this function or the convenience wrapper
     'buildMACAT'.

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

     preprocessedLoader(rdatafile, chip, labels = NULL, chromLocObj = NULL,
     rdafile = TRUE, tabfile = FALSE, labelfile = FALSE)

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

rdatafile: Complete name of the expression data file, or the 
          expression matrix

    chip: Identifier of the used microarray. To date only commercial
          Affymetrix microarrays are supported by MACAT

  labels: Classlabels of the samples, vector of same length as number
          of columns in expression matrix; alternatively complete name
          of textfile with one label per line

chromLocObj: Object of class 'chromLocation' specifying the genomic
          position, each probe on the array is mapped to. If not
          provided, it is build in the function using 'annotate''s
          function 'buildChromLocation'.

 rdafile: Logical; is first argument a saved R-file?

 tabfile: Logical; is first argument a tab-separated text file?

labelfile: Logical; is third argument a file with one label per line?

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

     List of class 'MACATData' with 6 components: 

geneName: Identifiers of genes/probe sets in expression data

geneLocation: Location of genes on their chromosome as distance from
          5'end in base pairs Negative numbers denote genes on the
          antisense strand.

chromosome: Chromosome of the respective gene. Components 'geneName',
          'geneLocation', and 'chromosome' are in the same order.

    expr: expression matrix with rows = genes and columns =
          samples/patients

  labels: (disease) subtype of each sample, has length = number of
          columns of expression matrix

    chip: Identifier for Microarray used for the experiments

_N_o_t_e:

     At present, 'macat' can only work with Affymetrix microarrays, for
     which an annotation package is installed on your system. Such
     annotation packages can either be obtained from the Bioconductor
     annotation packages repository or be constructed using the
     Bioconductor package 'AnnBuilder'. For an example, see the common
     annotation package 'hgu95av2'.

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

     MACAT development team

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

     'buildMACAT','read.table','stjd','stjude' in package 'stjudem'

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

      ## Not run: 
       # assume you have your HG-U95Av2 expression values in a
       # tab-separated text file, called 'foo.txt'
       mydata <- preprocessedLoader("foo.txt","hgu95av2",rdafile=FALSE,tabfile=TRUE)
      
     ## End(Not run)

