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, 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

 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:

     To date MACAT can only work with commercial Affymetrix
     microarrays, denoted by one the following identifiers: hu6800,
     hgu95av2, hgu95b, hgu95c, hgu95d, hgu95e,  hgu133a, hgu133b,
     mgu74av2, mgu74bv2, mgu74c, moe430a,  moe430b, rae230a, rae230b,
     rgu34a, rgu34b, rgu34c

_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)

