avpg                 package:GeneTS                 R Documentation

_A_v_e_r_a_g_e _P_e_r_i_o_d_o_g_r_a_m _f_o_r _M_u_l_t_i_p_l_e (_G_e_n_e_t_i_c) _T_i_m_e _S_e_r_i_e_s

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

     'avgp' calculates and plots the average periodogram as described
     in Wichert, Fokianos and Strimmer (2004).

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

     avgp(x, title = "untitled", plot = TRUE, angular = FALSE, ...)

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

       x: multiple (genetic) time series data (=matrix where each
          column corresponds to one time series)

   title: name of the data set

    plot: plot the average periodogram?

 angular: convert frequencies to angular frequencies?

     ...: arguments passed to 'plot' and to 'periodogram'

_D_e_t_a_i_l_s:

     The average periodogram is simply the frequency-wise average of
     the spectral density (as estimated by the Fourier transform) over
     all times series.  To calculate the average periodogram the
     function 'periodogram' is used. See Wichert, Fokianos and Strimmer
     (2004) for more details.

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

     A list object with the following components: 

    freq: A vector with the discrete Fourier frequencies (see
          'periodogram'). If the option angular=TRUE  then the output
          are angular frequencies (2*pi*f).

avg.spec: A vector with the average power spectral density at each
          frequency.

   title: Name of the data set underlying the average periodogram.


     The result is returned invisibly if 'plot' is true.

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

     Konstantinos Fokianos (<URL: http://www.ucy.ac.cy/~fokianos/>) and
     Korbinian Strimmer (<URL:
     http://www.stat.uni-muenchen.de/~strimmer/>).

_R_e_f_e_r_e_n_c_e_s:

     Wichert, S., Fokianos, K., and Strimmer, K. (2004).  Identifying
     periodically expressed transcripts in microarray time series data.
     _Bioinformatics_ *20*:5-20.

_S_e_e _A_l_s_o:

     'periodogram', 'spectrum'.

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

     # load GeneTS library
     library(GeneTS)

     # load data set
     data(caulobacter)

     # how many samples and how many genes?
     dim(caulobacter)

     # average periodogram
     avgp.caulobacter <- avgp(caulobacter, "Caulobacter")
     avgp.caulobacter

     # just compute and don't plot 
     avgp(caulobacter, "Caulobacter", plot=FALSE)

