read.marrayInfo         package:marrayInput         R Documentation

_C_r_e_a_t_e _o_b_j_e_c_t_s _o_f _c_l_a_s_s _m_a_r_r_a_y_I_n_f_o

_D_e_s_c_r_i_p_t_i_o_n:

     This function creates objects of class 'marrayInfo'. The
     'marrayInfo' class is used to store information regarding the
     target mRNA samples co-hybridized on the arrays or the spotted
     probe sequences (e.g. data frame of gene names, annotations, and
     other identifiers).

_U_s_a_g_e:

     read.marrayInfo(fname, info.id=NULL, labels=NULL, notes=fname, sep="\t",skip=0, quote="\"", ...)

_A_r_g_u_m_e_n_t_s:

   fname: the name of the file that stores information on target
          samples or probe sequences. This is usually a file obtained
          from a database.

 info.id: the column numbers in 'fname' that contain the required
          information.

  labels: the column number in 'fname' which contains the names that
          the user would like to use to label spots or arrays (e.g. for
          default titles in 'maPlot'.

   notes: object of class character, vector of explanatory text

     sep: the field separator character.  Values on each line of the
          file are separated by this character. The default is to read
          a tab delimited file.

    skip: the number of lines of the data file to skip before beginning
          to read data.

   quote: the set of quoting characters. By default, this is disable by
          setting `quote="\""'.

     ...: further arguments to 'scan'.

_D_e_t_a_i_l_s:

_V_a_l_u_e:

     An object of class 'marrayInfo'.

_A_u_t_h_o_r(_s):

     Jean Yang, yeehwa@stat.berkeley.edu

_R_e_f_e_r_e_n_c_e_s:

     http://www.bioconductor.org/

_E_x_a_m_p_l_e_s:

     datadir <- system.file("data", package="marrayInput")

     ## Reading target sample information
     swirl.samples <- read.marrayInfo(file.path(datadir, "SwirlSample.txt"))

     ## Reading probe sequence information
     swirl.gnames <- read.marrayInfo(file.path(datadir, "fish.gal"),
                                     info.id=4:5, labels=5, skip=21)

