read.exprSet             package:Biobase             R Documentation

_R_e_a_d _E_x_p_e_r_i_m_e_n_t_a_l _D_a_t_a _a_n_d _i_n_t_o _a_n '_e_x_p_r_S_e_t' _O_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     An exprSet object has a slot named 'exprs' for experimental data.
     'read.exprSet' reads the experimental data stored as a text file
     and then generates an exprSet object using the data. Data for
     other slots can be also read in as options.

_U_s_a_g_e:

     read.exprSet(exprs, se.exprs, phenoData, annotation, description, notes, seps = "\t")

_A_r_g_u_m_e_n_t_s:

   exprs: 'exprs' a character string for the name of the text file that
          stores the experimental data to be read in. The text file is
          assumed to be a delimited file with observed expression
          levels arranged in rows and columns. The first row of the
          file is sample names and the first column is gene names/ids.
          The file will be read in using read.table with header set to
          TRUE

se.exprs: 'se.exprs' a character stirng for the name of a delimited
          text file contains standard error estimates for the estimated
          expression in exprs. The file is of the same dimensions as
          'exprs'

phenoData: 'phenoData' a character string for the name of an optional
          file containing information for 'pData' slot of a phenoData
          object to be returned. If missing a default phenoData object
          with one covariate ranging from 1 to the number of columns of
          'exprs' will be provided

annotation: 'annotation' a character string for the name of an optional
          text file that contains a string identifying the annotation
          that may be used for the 'exprSet' instance

description: 'description' a character string for the name of an
          optional file containing MIAME information

   notes: 'notes' a character string for the name of an optional text
          file containing explanatory text

    seps: 'seps' a vector of character strings defining the delimitors
          used by 'exprs' and 'se.exprs'. The length of 'seps' can be 1
          when both file have the same delimiter or 'se.exprs' is
          missing or 2 other wise. The delimitor for 'exprs' is
          expected to be the first element

_D_e_t_a_i_l_s:

     If not missing, 'phenoData' will be read in using 'read.phenoData'
     and description using 'read.MIAME'. The help files of the two
     functions contain detailed descriptions of the two functions.

_V_a_l_u_e:

     This function returns an 'exprSet' object.

_N_o_t_e:

     This function is part of the Bioconductor project at Dana-Farber
     Cancer Institute to provide bioinformatics functionalities through
     R

_A_u_t_h_o_r(_s):

     Jianhua Zhang

_S_e_e _A_l_s_o:

     'exprSet', 'phenoData', 'MIAME', 'read.phenoData', 'read.MIAME'

_E_x_a_m_p_l_e_s:

     # Creating a test data
     testFile <- tempfile()
     data(geneData)
     write.table(geneData, testFile, quote = FALSE, sep = "\t", row.names =
     TRUE, col.names = TRUE)
     # Create an exprSet object using textFile
     eSet <- read.exprSet(testFile)
     eSet