readSpikeTypes         package:arrayQuality         R Documentation

_R_e_a_d _S_p_i_k_e _T_y_p_e_s _F_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     Read a table containing information about the doping control
     mixture used in the hybridization.

_U_s_a_g_e:

     readSpikeTypes(file = "DopingTypeFile2.txt", path = NULL, cy5col = "MassCy5", cy3col = "MassCy3", ...)

_A_r_g_u_m_e_n_t_s:

    file: A "character" string giving the name of the file specifying
          the doping controls used.

    path: A "character" string giving the directory containing the
          file. By default this is set to the current working directory
          (".").

  cy5col: A "character" string describing the name of the column
          corresponding to the controls labelled with Cy5.

  cy3col: A "character" string describing the name of the column
          corresponding to the controls labelled with Cy3.

     ...: Additional arguments passed to "readSpotTypes"

_D_e_t_a_i_l_s:

     The file is a text file with rows corresponding to doping controls
     and columns describing various experimental conditions. It must
     contain an oligo sequence identifier for each control, the spike
     type (e.g. Ambion or MJ) and the mass of each oligo spiked in each
     channel. By default, this function assumes that the mass unit are
     the same.

_V_a_l_u_e:

     A list of n matrices, each matrix containing information about a
     unique type of spiked controls.

_A_u_t_h_o_r(_s):

     Agnes Paquet

_E_x_a_m_p_l_e_s:

     datadir <- system.file("Meebo", package="arrayQuality")
     if (interactive())
     {
     spikes <-
     readSpikeTypes(file="StanfordDCV1.7complete.txt",path=datadir,cy5col="CY5.ng._MjDC_V1.7",cy3col="CY3.ng._MjDC_V1.7")
     }

