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")
     }

