read.genepix           package:phyloarray           R Documentation

_R_e_a_d_i_n_g _g_e_n_e_p_i_x-_f_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     Read a genepix-file ('.gpr') and stores result in a list
     containing 'header' and 'data'.

_U_s_a_g_e:

       read.genepix2(file, temperature=42, buffer=data.frame(na=0.97, f=35))

_A_r_g_u_m_e_n_t_s:

    file: The name of the file to be read. The extension should be
          given.

temperature: The temperature of hybridization (or washing) step. Since
          there's a focus on melting curves, this is important and the
          value given here will be added to the header.

  buffer: Buffer contents used during hybridization (or washing). This
          is not used anywhere yet, but it might e.g. to calculate the
          theoretical melting/annealing temperature based on the
          sequence and the buffer content. 'na' is the salt
          (Na)-content and 'f' the formamide concentration (in
          percent).

_V_a_l_u_e:

     The function returns a list containing: 

  Header: A list with the header fields of the '.gpr'-file, with
          additional information concerning the hybridization
          temperature and buffer contents (given as arguments to the
          function.

    Data: A data matrix with the data in a '.gpr'-file. This includes
          median and mean values for fore- and background, as well as
          probe ID's, standard deviations, X and Y       values etc.

_N_o_t_e:

     Since there is a function read.genepix in 'sma', this function has
     been called 'read.genepix2'. It must be noted that for new
     versions of genepix, the function in the 'sma'-package doesn't
     work (since more columns are added). This function works for both,
     but I have really no idea how the future will be... Anyway I tried
     to make it as general as possible.

     Data from other image processing software (e.g. Spot) may be
     imported using the package 'sma'. In that case, one should know
     the names of the fields of the red/green signals etc.

_A_u_t_h_o_r(_s):

     Kurt Sys (kurt.sys@advalvas.be)

_R_e_f_e_r_e_n_c_e_s:

_S_e_e _A_l_s_o:

     'Scandataraw' 'Phylodata'

     'init.data'

_E_x_a_m_p_l_e_s:

       # There are this-is-escaped-codenormal-bracket36bracket-normal-files in the data-section of this package
       #
       # scan1 <- read.genepix2("<file_scan.at.22degrees>", temperature=22)
       # ...
       # scan3 <- read.genepix2("<file_scan.at.58degrees>", temperature=58)
       #
       # 
       # or, e.g.:
       #
       # scan <- 1
       # for (t in c(22+0:2*18)) normal-bracket37bracket-normal
       #   assign(paste("scan", slide, sep=""),
       #          read.genepix2(paste("wash", t, ".gpr", sep=""), temperature=t))
       #   scan <- scan+1
       # normal-bracket37bracket-normal

