read.marrayRaw          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_R_a_w"

_D_e_s_c_r_i_p_t_i_o_n:

     This function reads in cDNA microarray data from a directory and
     creates objects of class '"marrayRaw"' from spot quantification
     data files obtained from image analysis software or databases.

_U_s_a_g_e:

     read.marrayRaw(fnames, path=".", name.Gf, name.Gb=NULL, name.Rf,
     name.Rb=NULL,name.W=NULL, layout=NULL, gnames=NULL, targets=NULL,
     notes=NULL, skip=0, sep="       ", quote="\"",...)

     read.GenePix(fnames = NULL, path = ".", name.Gf = "F532 Mean",
     name.Gb ="B532 Median", name.Rf = "F635 Mean", name.Rb = "B635 Median",
     name.W =NULL, layout = NULL, gnames = NULL, targets = NULL,
     notes = NULL, skip=0, sep = "   ", quote = "\"", ...)

     read.SMDfnames = NULL, path = ".", name.Gf = "CH1I_MEAN",
                      name.Gb = "CH1B_MEDIAN", name.Rf = "CH2I_MEAN",
                      name.Rb = "CH2B_MEDIAN", name.W = NULL, layout =
                      NULL, gnames = NULL, targets = NULL, notes = NULL,
                      skip = 0, sep = "\t", quote = "", ...)

     read.Spot(fnames = NULL, path = ".", name.Gf = "Gmean",
     name.Gb = "morphG", name.Rf = "Rmean", name.Rb = "morphR",
     name.W = NULL, layout = NULL, gnames = NULL, targets = NULL,
     notes = NULL, skip = 0, sep = " ", quote = "\"", ...)

     widget.marrayRawext = c("spot", "xls", "gpr"), skip = 0, sep = "\t",
                      quote = "", ...)

_A_r_g_u_m_e_n_t_s:

  fnames: a vector of character strings containing the file names of
          each spot quantification data file.  These typically end in
          '.spot' for the software 'Spot' or '.gpr' for the software
          'GenePix'.

    path: a character string representing the data directory. By
          default this is set to the current working directory ("."). 
          In the case where 'fnames' contains the full path name, path
          should be set to NULL.

 name.Gf: character string for the column header for green foreground
          intensities.

 name.Gb: character string for the column header for green background
          intensities.

 name.Rf: character string for the column header for red foreground
          intensities.

 name.Rb: character string for the column header for red background
          intensities.

  name.W: character string for the column header for spot quality
          weights.

  layout: object of class '"marrayLayout"', containing microarray
          layout parameters.

  gnames: object of class '"marrayInfo"' containing probe sequence
          information.

 targets: object of class '"marrayInfo"' containing target sample
          information.

   notes: object of class '"character"', vector of explanatory text.

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

     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.

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

     ...: further arguments to 'scan'.

_D_e_t_a_i_l_s:

_V_a_l_u_e:

     An object of class '"marrayRaw"'.

_A_u_t_h_o_r(_s):

     Jean Yang, yeehwa@stat.berkeley.edu

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.bioconductor.org/>.

_S_e_e _A_l_s_o:

     'scan', 'read.marrayLayout', 'read.marrayInfo'

_E_x_a_m_p_l_e_s:

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

     skip <-  grep("Row", readLines(file.path(datadir,"fish.gal"), n=100)) - 1

     swirl.layout <- read.marrayLayout(ngr=4, ngc=4, nsr=22, nsc=24)

     swirl.targets <- read.marrayInfo(file.path(datadir, "SwirlSample.txt"))

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

     x <-  maInfo(swirl.gnames)[,1]
     y <- rep(0, maNspots(swirl.layout))
     y[x == "control"] <- 1
     slot(swirl.layout, "maControls") <- as.factor(y)

     fnames <- dir(path=datadir,pattern=paste("*", "spot", sep="\."))
     swirl<- read.Spot(fnames, path=datadir,
                            layout = swirl.layout,
                            gnames = swirl.gnames,
                            targets = swirl.targets)

