spkAll               package:spkTools               R Documentation

_S_p_i_k_e-_i_n _F_u_n_c_t_i_o_n_s _W_r_a_p_p_e_r

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

     A wrapper for the functions contained in the spkTools package,
     which calls each function.

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

     spkAll(object, label, model=expr~spike+probe+array, fc=NULL, tol=3,
     xrngs=NULL, yrngs=NULL, cuts=c(.6,.99), potQuantile=.995,
     gnn=c(25,100,10000), pch=".", output="eps")

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

  object: a SpikeInExpressionSet object

   label: a character string to insert into the graphs and tables
          produced

   model: model to be passed to spkAnova

      fc: the fold change for which fold change plots will be produced

     tol: the number of digits after the decimal point in fc

   xrngs: ranges for the x-axis of each plot. d=density, s=slope,
          v=box, m=M vs A

   yrngs: ranges for the y-axis of each plot. d=density, s=slope,
          v=box, m=M vs A

    cuts: quantiles used to make the low, medium, and high bins

potQuantile: the desired quantile to compute the probability of being
          above

     gnn: a vector of 3 numbers passed to spkGNN: the desired number of
          true positives, the number of truly expressed genes, and the
          number of truly unexpressed genes

     pch: plotting point to be used in spkSlope

  output: the format in which to save the plots produced. Options are
          "pdf" and "eps"

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

     The full complement of plots and tables described in the vignette
     are created and saved in the current working directory.

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

     Matthew N. McCall

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

     data(affy)
     spkAll(affy, label="affy", fc=2)

