read.marrayLayout           package:marray           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_L_a_y_o_u_t

_D_e_s_c_r_i_p_t_i_o_n:

     This function creates objects of class 'marrayLayout' to store
     layout parameters for  two-color cDNA microarrays.

_U_s_a_g_e:

     read.marrayLayout(fname = NULL, ngr, ngc, nsr, nsc, pl.col = NULL, ctl.col = NULL, sub.col = NULL, notes = fname, skip, sep = "\t", quote = "\"", ...)

_A_r_g_u_m_e_n_t_s:

   fname: the name of the file that stores plate and control
          information. This is usually a file obtained from a database.

     ngr: the number of rows of grids per image.

     ngc: the number of columns of grids per image.

     nsr: the number of rows of spots per grid.

     nsc: the number of columns of spots per grid.

  pl.col: the column number in 'fname' that contains plate information.

 ctl.col: the column number in 'fname' that contains control
          information.

 sub.col: the column number in 'fname' that contains full ID
          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 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 disable by
          setting `quote="\""'.

     ...: further arguments to 'scan'.

_D_e_t_a_i_l_s:

_V_a_l_u_e:

     An object of class 'marrayLayout'.

_N_o_t_e:

_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("swirldata", package="marray")

     ### Reading in control information from file
     skip <-  grep("Row", readLines(file.path(datadir,"fish.gal"), n=100)) - 1
     swirl.layout <- read.marrayLayout(fname=file.path(datadir,"fish.gal"), ngr=4, ngc=4,
     nsr=22, nsc=24, ctl.col=4, skip=skip)

     ### Setting control information.
     swirl.gnames <- read.marrayInfo(file.path(datadir,"fish.gal"), info.id=4:5, labels=5, skip=21)
     x <-  maInfo(swirl.gnames)[,1]
     y <- rep(0, maNspots(swirl.layout))
     y[x == "control"] <- 1
     slot(swirl.layout, "maControls") <- as.factor(y)