read.genepix               package:sma               R Documentation

_R_e_a_d_i_n_g _i_n _D_a_t_a _G_e_n_e_r_a_t_e_d _b_y _t_h_e _I_m_a_g_e _A_n_a_l_y_s_i_s _P_a_c_k_a_g_e _G_e_n_e_P_i_x.

_D_e_s_c_r_i_p_t_i_o_n:

     Reads in a data file in table format and creates a data frame with
     the same number of rows as there are lines in the file, and the
     same number of columns as there are fields in the file.
      `read.genepix' reads in the data file generated by the software
     "GenePix".

_U_s_a_g_e:

     read.genepix(name, dir = ".", sep = "\t", header = TRUE, skip = 26, gpname = c("Block", "Col", "Row", "Name", "ID", "X","Y", "Dia", "Rmed", "Rmean", "RSD", "Rbmed", "Rbmean", "RbSD", "Rb1SD", "Rb2SD", "Rbsat","Gmed", "Gmean", "GSD", "Gbmed", "Gbmean", "GbSD", "Gb1SD", "Gb2SD", "Gbsat", "ratiomed", "ratiomean", "medratio", "meanratio", "ratiosd", "Rratio", "RegR2", "FPixels", "BPixels", "summed", "summean", "logratio", "Rmedc", "Gmedc", "Rmeanc", "Gmedc", "flags"),...) 

_A_r_g_u_m_e_n_t_s:

    name: character string naming the data file from which to read the
          data. 

     dir: character string naming the directory that contains the data
          file.

     sep: the field separator (single  character),  often  "\t"  for
          tab delimited fields.  If omitted,  any  amount  of white
          space (blanks or tabs) can separate the fields.  To read 
          fixed  format files, make  sep  a  numeric vector giving the
          initial columns of the fields. 

  header: logical flag: if TRUE, then the first line of the file is
          used as the variable names of the resulting data frame. 

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

  gpname: A vector of column names. SOme of the column names from
          genepix contain non standard characters, so useful to
          redefine to something R likes to use. Also newer versions of
          genepix have more columns

     ...: parameters for read.table may also be supplied as arguments
          to the function (see  'read.table').  

_V_a_l_u_e:

     as in 'read.table', a data frame ('data.frame') containing a
     representation of the data in the file.

_S_e_e _A_l_s_o:

     'read.table', 'data.frame', 'read.spot'.

