volcano               package:maanova               R Documentation

_V_o_l_c_a_n_o _p_l_o_t _f_o_r _F _t_e_s_t _r_e_s_u_l_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function generates a volcano-like plot given the F test
     results.

_U_s_a_g_e:

     volcano(matestobj, threshold=c(0.001,0.05),
             method=c("unadj","unadj"), title="Volcano Plot",
             highlight.flag=TRUE, onScreen=TRUE)

_A_r_g_u_m_e_n_t_s:

matestobj: An object of class 'matest'.

threshold: A vector of three double values to indicate the thresholds
          for three F tests. The values should be between 0 and 1. Note
          that you need to put three values here even if you don't have
          all three F tests in matestobj.

  method: A flag indicates to use which P values to generate the plot
          and select genes. This is a vector with three elements, which
          corresponds to three F tests. Each element should be one of
          the following five selections:

        "_u_n_a_d_j" Unadjusted tabulated P values.

        "_n_o_m_i_n_a_l" Nominal permutation P values.

        "_f_w_e_r" FWER one-step adjusted P values.

        "_f_d_r" FDR adjusted tabulated P values.

        "_f_d_r_p_e_r_m" FDR adjusted nominal permutation P values.

          Default value is c("unadj", "unadj") which means to use
          tabulated P values for all tests.

          Note that you need to put three values here even if you don't
          have all three F tests in matestobj.

   title: Figure title. Default is "Volcano Plot".

highlight.flag: A logical value to indicate whether to highlight the
          genes with bad spots or not.

onScreen: A logical value to represent whether to display the plots on
          screen or not. If TRUE, the figure will be plotted on the
          screen. Otherwise, it will plot the figure on the current
          device. Default is TRUE.

_D_e_t_a_i_l_s:

     This function allows one to visualize the results from the F or T 
     tests. The figure looks like an erupting volcano. There will be
     one plot For F-test result and multiple plots for T-test result,
     each plot corresponds to one T-test. You must have F1 test result
     in the input object in order to do volcano plot. 

     On the plot, blue dots are the genes selected by the F1 test. The
     y-axis value is -log10(P-value) for the F1 test and x-axis value
     is proportional to the fold changes.  A horizontal line represents
     the significance threshold of the F1 test. The red dots are the
     genes selected by the Fs test (if there's Fs test result).  If
     there is flag information in the data and the user wants to
     highlight the flagged genes, the genes with any bad spots will be
     circled by a black circle.

_V_a_l_u_e:

     For F-test volcano plot, it returns an object which is a list of
     the following four fields:  

  idx.F1: The significant genes selected by F1 test.

  idx.Fs: The significant genes selected by Fs test.

 idx.all: The significant genes selected by all four F tests.


     For T-test volcano plot, it returns an array of the above object.
     Each element in the array corresponds to one T-test.

_A_u_t_h_o_r(_s):

     Hao Wu

_E_x_a_m_p_l_e_s:

     ## Not run: 
     data(abf1)
     fit.full.mix <- fitmaanova(abf1, formula = ~Strain+Sample, 
         random = ~Sample)
     ftest.all = matest(abf1, fit.full.mix, test.method=c(1,1),
         shuffle.method="sample", term="Strain", n.perm= 100)
     volcano(ftest.all)
     ## End(Not run)

