geneprofile             package:maanova             R Documentation

_E_x_p_r_e_s_s_i_o_n _p_l_o_t _f_o_r _s_e_l_e_c_t_e_d _g_e_n_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function generate a plot with many lines. Each line
     represents a gene. The y-axis is the estimated expression level
     for the given factor from ANOVA model. The x-axis is for the
     levels of the give factor, e.g., different strains.

_U_s_a_g_e:

     geneprofile(anovaobj, term, geneidx,
                 col="blue", type="b", ylim, xlab, ylab, ...)

_A_r_g_u_m_e_n_t_s:

anovaobj: An object of class 'maanova'. It should be the result from
          'fitmaanova'.

    term: The terms to be plotted.

 geneidx: The index of genes to be plotted.

     col: The color to be used in plot.

    type: The line type.

    ylim: Y-axis limit.

    xlab: X-axis label.

    ylab: Y-axis label.

     ...: Other parameters to be passed to 'plot'.

_A_u_t_h_o_r(_s):

     Hao Wu

_E_x_a_m_p_l_e_s:

     # load in data
     data(abf1)
     # fit the anova model
     ## Not run: 
     fit.fix = fitmaanova(abf1,formula = ~Strain)
     # test Strain effect 
     test.fix = matest(abf1, fit.fix, term="Strain",n.perm= 1000)
     # pick significant genes - pick the genes selected by Fs test
     idx <- volcano(test.fix)$idx.Fs
     geneprofile(fit.fix, "Strain", idx)
     ## End(Not run)

