init.data             package:phyloarray             R Documentation

_I_n_i_t_i_a_l_i_z_e _d_a_t_a

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

     Read the important fields of the several raw data-objects and
     store them in a new object (with class "phyloarray"). This
     function also reads the temperatures from the headers.

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

       init.data2()

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

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

     The function returns an object of class 'phyloarray'. It is a list
     with values R (red signal), G (green signal), Rb (red background
     signal), Gb (green background signal), Rsd (standard deviation of
     red signal) and Gsd (standard deviation of green signal). The
     standard deviation values are used to mark bad spots (based on
     sd/signal). The list contains also X- and Y-values of the spots
     (to calculate background, if necessary) and the ID's of the
     probes. Each field R, G, Rb, Gb, Rsd and Gsd is a datamatrix with
     in the rows the values for the different probes and in the columns
     the different temperatures. To a larger extent, the columns may be
     other factors to (such as time-related values), but they are
     designed to be used for making melting curves and analysis on the
     melting curves.

_N_o_t_e:

     Since there is a function 'init.data' in 'sma', this function has
     been calles 'init.data2'. It is largely the same function, but
     some fields are added to make the phylogenetic analysis of melting
     curves more easy.

     Some examples of basic handling of an object of class phyloarray
     is in the help-file 'Phylodata'

_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'

     'read.genepix'

     'getprobes'

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

       # load the saved raw data from this package:
       # data(Scandataraw)

       # scans <- init.data2()

       # Are you creating a new data matrix or adding new array data
       # to a prexisting data matrix? 
       # Enter "n" for creating  and "a" for adding new array data: n
       # Do the names of all your datasets have the following format: 
       # prefix1, prefix2, prefix3?, ... Here prefix can be any name, 
       # but the suffixes must be integers 1,2, ..., # of arrays. 
       # Enter "y" for yes, "n" for no: y
       # Enter the prefix:scan
       # Enter the number of arrays to be processed:3
       # Enter the name of Cy3 raw data: Gmed
       # Enter the name of Cy3 background: Gbmed
       # Enter the name of Cy3 intensity standard deviation: GSD
       # Enter the name of Cy5 raw data: Rmed
       # Enter the name of Cy5 background: Rbmed
       # Enter the name of Cy5 intensity standard deviation: RSD
       # Enter the name of the ID/probenames field: ID
       # Enter the X values for probe positions: Column
       # Enter the Y values for probe positions: Row
       # Finished creating the dataset.


       # load data this-is-escaped-codenormal-bracket27bracket-normal, i.e. this-is-escaped-codenormal-bracket28bracket-normal
       data(Phylodata)

       names(scans)

       attributes(scans)

