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Last data update: 2014.03.03

R: Dominant Frequencies in Multiple (Genetic) Time Series

dominant.freqs

R Documentation

Dominant Frequencies in Multiple (Genetic) Time Series

Description

dominant.freqs returns the m dominant frequencies (highest peaks) in each of the periodogram computed for the individual time series.

Usage

dominant.freqs(x, m=1, ...)

Arguments

`x`	multivariate (genetic) time series (each column of this matrix corresponds to a separate variable/time series), or a vector with a single time series
`m`	number of dominant frequences
`...`	arguments passed to `periodogram`

Value

A matrix (or vector, if only 1 time series is considered) with the dominant frequencies. In a matrix, each column corresponds to one time series.

Author(s)

Konstantinos Fokianos (http://www.ucy.ac.cy/~fokianos/) and Korbinian Strimmer (http://strimmerlab.org).

Examples

# load GeneCycle library
library("GeneCycle")

# load data set
data(caulobacter)

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

# first three dominant frequencies for each gene
dominant.freqs(caulobacter, 3)

# first four dominant frequencies for gene no. 1000
dominant.freqs(caulobacter[,1000], 4)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GeneCycle)
Loading required package: MASS
Loading required package: longitudinal
Loading required package: corpcor
Loading required package: fdrtool
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GeneCycle/dominant.freqs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dominant.freqs
> ### Title: Dominant Frequencies in Multiple (Genetic) Time Series
> ### Aliases: dominant.freqs
> ### Keywords: ts
> 
> ### ** Examples
> 
> # load GeneCycle library
> library("GeneCycle")
> 
> # load data set
> data(caulobacter)
> 
> # how many samples and how many genes?
> dim(caulobacter)
[1]   11 1444
> 
> # first three dominant frequencies for each gene
> dominant.freqs(caulobacter, 3)
           [,1]       [,2]       [,3]       [,4]       [,5]       [,6]
[1,] 0.09090909 0.09090909 0.09090909 0.09090909 0.09090909 0.09090909
[2,] 0.27272727 0.18181818 0.18181818 0.18181818 0.18181818 0.18181818
[3,] 0.36363636 0.45454545 0.45454545 0.36363636 0.27272727 0.27272727
          [,7]       [,8]       [,9]      [,10]      [,11]      [,12]
[1,] 0.3636364 0.09090909 0.09090909 0.09090909 0.09090909 0.27272727
[2,] 0.2727273 0.18181818 0.45454545 0.18181818 0.36363636 0.45454545
[3,] 0.1818182 0.27272727 0.27272727 0.36363636 0.18181818 0.09090909
          [,13]     [,14]      [,15]      [,16]      [,17]      [,18]
[1,] 0.09090909 0.3636364 0.18181818 0.09090909 0.09090909 0.09090909
[2,] 0.36363636 0.4545455 0.09090909 0.36363636 0.18181818 0.45454545
[3,] 0.18181818 0.1818182 0.27272727 0.18181818 0.36363636 0.27272727
          [,19]      [,20]      [,21]     [,22]      [,23]      [,24]
[1,] 0.09090909 0.27272727 0.36363636 0.3636364 0.09090909 0.45454545
[2,] 0.18181818 0.18181818 0.18181818 0.1818182 0.18181818 0.09090909
[3,] 0.27272727 0.09090909 0.09090909 0.4545455 0.27272727 0.27272727
          [,25]      [,26]      [,27]      [,28]      [,29]      [,30]
[1,] 0.18181818 0.45454545 0.09090909 0.27272727 0.18181818 0.09090909
[2,] 0.09090909 0.18181818 0.27272727 0.09090909 0.09090909 0.18181818
[3,] 0.27272727 0.09090909 0.18181818 0.45454545 0.27272727 0.27272727
          [,31]     [,32]      [,33]      [,34]      [,35]      [,36]
[1,] 0.09090909 0.2727273 0.09090909 0.45454545 0.09090909 0.09090909
[2,] 0.27272727 0.1818182 0.45454545 0.09090909 0.27272727 0.18181818
[3,] 0.18181818 0.4545455 0.36363636 0.27272727 0.45454545 0.45454545
          [,37]      [,38]      [,39]     [,40]      [,41]      [,42]
[1,] 0.18181818 0.09090909 0.09090909 0.2727273 0.36363636 0.27272727
[2,] 0.09090909 0.18181818 0.18181818 0.1818182 0.27272727 0.18181818
[3,] 0.27272727 0.27272727 0.27272727 0.3636364 0.09090909 0.09090909
          [,43]      [,44]      [,45]     [,46]      [,47]      [,48]
[1,] 0.09090909 0.09090909 0.27272727 0.2727273 0.18181818 0.27272727
[2,] 0.45454545 0.18181818 0.09090909 0.1818182 0.27272727 0.18181818
[3,] 0.27272727 0.27272727 0.45454545 0.4545455 0.09090909 0.09090909
          [,49]      [,50]     [,51]      [,52]     [,53]     [,54]     [,55]
[1,] 0.27272727 0.09090909 0.1818182 0.09090909 0.3636364 0.2727273 0.3636364
[2,] 0.18181818 0.18181818 0.2727273 0.18181818 0.2727273 0.1818182 0.2727273
[3,] 0.09090909 0.27272727 0.3636364 0.45454545 0.4545455 0.4545455 0.1818182
          [,56]      [,57]      [,58]      [,59]      [,60]      [,61]
[1,] 0.45454545 0.27272727 0.09090909 0.09090909 0.09090909 0.18181818
[2,] 0.36363636 0.09090909 0.18181818 0.45454545 0.18181818 0.09090909
[3,] 0.09090909 0.18181818 0.45454545 0.18181818 0.27272727 0.27272727
          [,62]      [,63]      [,64]      [,65]      [,66]      [,67]
[1,] 0.27272727 0.09090909 0.09090909 0.09090909 0.09090909 0.09090909
[2,] 0.09090909 0.36363636 0.18181818 0.18181818 0.45454545 0.18181818
[3,] 0.18181818 0.45454545 0.27272727 0.45454545 0.18181818 0.45454545
         [,68]     [,69]      [,70]     [,71]      [,72]      [,73]      [,74]
[1,] 0.2727273 0.1818182 0.27272727 0.1818182 0.18181818 0.18181818 0.18181818
[2,] 0.4545455 0.2727273 0.36363636 0.2727273 0.45454545 0.45454545 0.09090909
[3,] 0.1818182 0.3636364 0.09090909 0.4545455 0.09090909 0.09090909 0.45454545
         [,75]      [,76]      [,77]      [,78]      [,79]      [,80]
[1,] 0.1818182 0.09090909 0.09090909 0.09090909 0.09090909 0.09090909
[2,] 0.4545455 0.45454545 0.18181818 0.36363636 0.18181818 0.18181818
[3,] 0.2727273 0.18181818 0.45454545 0.45454545 0.27272727 0.27272727
          [,81]     [,82]     [,83]      [,84]      [,85]      [,86]      [,87]
[1,] 0.18181818 0.4545455 0.4545455 0.09090909 0.36363636 0.45454545 0.27272727
[2,] 0.45454545 0.1818182 0.1818182 0.36363636 0.45454545 0.09090909 0.18181818
[3,] 0.09090909 0.2727273 0.2727273 0.45454545 0.09090909 0.27272727 0.09090909
         [,88]     [,89]     [,90]     [,91]      [,92]      [,93]      [,94]
[1,] 0.4545455 0.4545455 0.4545455 0.3636364 0.45454545 0.09090909 0.09090909
[2,] 0.3636364 0.2727273 0.3636364 0.1818182 0.09090909 0.45454545 0.45454545
[3,] 0.1818182 0.3636364 0.1818182 0.4545455 0.18181818 0.27272727 0.36363636
          [,95]      [,96]      [,97]      [,98]      [,99]     [,100]
[1,] 0.27272727 0.09090909 0.09090909 0.27272727 0.18181818 0.18181818
[2,] 0.09090909 0.36363636 0.45454545 0.09090909 0.09090909 0.09090909
[3,] 0.18181818 0.27272727 0.36363636 0.45454545 0.36363636 0.36363636
         [,101]     [,102]    [,103]     [,104]     [,105]     [,106]    [,107]
[1,] 0.09090909 0.09090909 0.4545455 0.45454545 0.27272727 0.09090909 0.4545455
[2,] 0.27272727 0.18181818 0.2727273 0.18181818 0.09090909 0.18181818 0.2727273
[3,] 0.18181818 0.27272727 0.1818182 0.09090909 0.36363636 0.27272727 0.3636364
        [,108]     [,109]    [,110]     [,111]     [,112]    [,113]     [,114]
[1,] 0.4545455 0.09090909 0.4545455 0.09090909 0.09090909 0.1818182 0.09090909
[2,] 0.3636364 0.45454545 0.1818182 0.27272727 0.45454545 0.4545455 0.18181818
[3,] 0.1818182 0.18181818 0.3636364 0.36363636 0.36363636 0.2727273 0.27272727
         [,115]    [,116]    [,117]    [,118]    [,119]     [,120]     [,121]
[1,] 0.09090909 0.4545455 0.2727273 0.1818182 0.4545455 0.09090909 0.45454545
[2,] 0.27272727 0.3636364 0.3636364 0.4545455 0.1818182 0.45454545 0.09090909
[3,] 0.18181818 0.1818182 0.4545455 0.2727273 0.3636364 0.27272727 0.36363636
         [,122]    [,123]     [,124]    [,125]     [,126]     [,127]     [,128]
[1,] 0.09090909 0.4545455 0.09090909 0.1818182 0.18181818 0.09090909 0.36363636
[2,] 0.45454545 0.2727273 0.18181818 0.2727273 0.27272727 0.36363636 0.09090909
[3,] 0.36363636 0.3636364 0.27272727 0.4545455 0.09090909 0.18181818 0.27272727
         [,129]     [,130]    [,131]     [,132]     [,133]     [,134]
[1,] 0.36363636 0.18181818 0.2727273 0.27272727 0.09090909 0.09090909
[2,] 0.45454545 0.09090909 0.1818182 0.18181818 0.18181818 0.45454545
[3,] 0.09090909 0.45454545 0.4545455 0.09090909 0.27272727 0.27272727
         [,135]    [,136]     [,137]     [,138]     [,139]     [,140]
[1,] 0.09090909 0.1818182 0.09090909 0.09090909 0.09090909 0.45454545
[2,] 0.27272727 0.4545455 0.27272727 0.18181818 0.45454545 0.18181818
[3,] 0.45454545 0.2727273 0.18181818 0.45454545 0.18181818 0.09090909
         [,141]     [,142]     [,143]     [,144]     [,145]    [,146]
[1,] 0.09090909 0.09090909 0.09090909 0.45454545 0.09090909 0.4545455
[2,] 0.45454545 0.18181818 0.36363636 0.27272727 0.36363636 0.2727273
[3,] 0.18181818 0.27272727 0.18181818 0.09090909 0.18181818 0.1818182
         [,147]     [,148]     [,149]     [,150]    [,151]     [,152]
[1,] 0.09090909 0.09090909 0.09090909 0.18181818 0.4545455 0.09090909
[2,] 0.27272727 0.18181818 0.18181818 0.09090909 0.1818182 0.45454545
[3,] 0.18181818 0.27272727 0.27272727 0.27272727 0.2727273 0.18181818
         [,153]     [,154]     [,155]     [,156]    [,157]     [,158]
[1,] 0.09090909 0.09090909 0.45454545 0.09090909 0.1818182 0.36363636
[2,] 0.18181818 0.45454545 0.09090909 0.18181818 0.2727273 0.27272727
[3,] 0.45454545 0.27272727 0.18181818 0.27272727 0.4545455 0.09090909
         [,159]     [,160]     [,161]     [,162]     [,163]    [,164]    [,165]
[1,] 0.09090909 0.36363636 0.09090909 0.18181818 0.09090909 0.4545455 0.3636364
[2,] 0.18181818 0.27272727 0.45454545 0.09090909 0.18181818 0.3636364 0.1818182
[3,] 0.27272727 0.09090909 0.36363636 0.36363636 0.45454545 0.1818182 0.4545455
        [,166]    [,167]     [,168]    [,169]     [,170]     [,171]    [,172]
[1,] 0.3636364 0.4545455 0.09090909 0.4545455 0.09090909 0.09090909 0.1818182
[2,] 0.4545455 0.3636364 0.36363636 0.1818182 0.45454545 0.45454545 0.3636364
[3,] 0.1818182 0.1818182 0.18181818 0.2727273 0.36363636 0.27272727 0.4545455
         [,173]     [,174]     [,175]     [,176]     [,177]     [,178]
[1,] 0.09090909 0.09090909 0.36363636 0.36363636 0.09090909 0.09090909
[2,] 0.18181818 0.27272727 0.09090909 0.18181818 0.36363636 0.18181818
[3,] 0.27272727 0.45454545 0.45454545 0.09090909 0.18181818 0.45454545
        [,179]     [,180]    [,181]    [,182]     [,183]     [,184]    [,185]
[1,] 0.2727273 0.09090909 0.1818182 0.4545455 0.09090909 0.45454545 0.1818182
[2,] 0.4545455 0.36363636 0.3636364 0.3636364 0.18181818 0.18181818 0.3636364
[3,] 0.3636364 0.45454545 0.4545455 0.1818182 0.27272727 0.09090909 0.4545455
        [,186]     [,187]     [,188]     [,189]    [,190]     [,191]    [,192]
[1,] 0.4545455 0.18181818 0.27272727 0.09090909 0.3636364 0.09090909 0.1818182
[2,] 0.3636364 0.36363636 0.45454545 0.27272727 0.2727273 0.18181818 0.4545455
[3,] 0.2727273 0.09090909 0.09090909 0.45454545 0.1818182 0.27272727 0.3636364
         [,193]     [,194]     [,195]     [,196]     [,197]     [,198]
[1,] 0.18181818 0.09090909 0.18181818 0.09090909 0.09090909 0.36363636
[2,] 0.09090909 0.27272727 0.45454545 0.36363636 0.27272727 0.09090909
[3,] 0.27272727 0.18181818 0.09090909 0.45454545 0.18181818 0.27272727
         [,199]     [,200]     [,201]     [,202]    [,203]     [,204]    [,205]
[1,] 0.36363636 0.18181818 0.18181818 0.45454545 0.3636364 0.45454545 0.1818182
[2,] 0.09090909 0.36363636 0.45454545 0.09090909 0.2727273 0.09090909 0.2727273
[3,] 0.45454545 0.09090909 0.09090909 0.27272727 0.4545455 0.27272727 0.3636364
         [,206]     [,207]     [,208]     [,209]     [,210]     [,211]
[1,] 0.09090909 0.09090909 0.18181818 0.09090909 0.36363636 0.09090909
[2,] 0.27272727 0.36363636 0.27272727 0.18181818 0.18181818 0.18181818
[3,] 0.36363636 0.27272727 0.09090909 0.36363636 0.09090909 0.27272727
         [,212]    [,213]    [,214]     [,215]     [,216]    [,217]     [,218]
[1,] 0.09090909 0.1818182 0.3636364 0.18181818 0.09090909 0.4545455 0.45454545
[2,] 0.18181818 0.2727273 0.4545455 0.45454545 0.27272727 0.3636364 0.09090909
[3,] 0.27272727 0.4545455 0.2727273 0.09090909 0.45454545 0.2727273 0.18181818
         [,219]     [,220]     [,221]    [,222]    [,223]     [,224]     [,225]
[1,] 0.09090909 0.09090909 0.09090909 0.1818182 0.1818182 0.09090909 0.18181818
[2,] 0.18181818 0.18181818 0.18181818 0.4545455 0.4545455 0.18181818 0.45454545
[3,] 0.45454545 0.27272727 0.45454545 0.3636364 0.2727273 0.27272727 0.09090909
        [,226]     [,227]     [,228]     [,229]     [,230]     [,231]
[1,] 0.4545455 0.18181818 0.45454545 0.18181818 0.09090909 0.09090909
[2,] 0.1818182 0.36363636 0.36363636 0.27272727 0.36363636 0.18181818
[3,] 0.2727273 0.09090909 0.09090909 0.09090909 0.27272727 0.27272727
         [,232]     [,233]     [,234]     [,235]     [,236]    [,237]
[1,] 0.09090909 0.09090909 0.09090909 0.18181818 0.09090909 0.2727273
[2,] 0.36363636 0.36363636 0.18181818 0.09090909 0.27272727 0.1818182
[3,] 0.45454545 0.27272727 0.45454545 0.27272727 0.18181818 0.4545455
         [,238]     [,239]     [,240]     [,241]     [,242]     [,243]
[1,] 0.27272727 0.09090909 0.09090909 0.18181818 0.09090909 0.09090909
[2,] 0.18181818 0.45454545 0.18181818 0.36363636 0.45454545 0.18181818
[3,] 0.09090909 0.27272727 0.45454545 0.09090909 0.36363636 0.36363636
         [,244]    [,245]    [,246]     [,247]     [,248]     [,249]    [,250]
[1,] 0.18181818 0.1818182 0.3636364 0.09090909 0.45454545 0.18181818 0.4545455
[2,] 0.09090909 0.2727273 0.4545455 0.18181818 0.36363636 0.09090909 0.1818182
[3,] 0.45454545 0.4545455 0.2727273 0.27272727 0.09090909 0.45454545 0.2727273
         [,251]    [,252]     [,253]     [,254]     [,255]     [,256]
[1,] 0.09090909 0.1818182 0.09090909 0.09090909 0.09090909 0.09090909
[2,] 0.18181818 0.4545455 0.18181818 0.18181818 0.18181818 0.18181818
[3,] 0.27272727 0.3636364 0.27272727 0.27272727 0.27272727 0.27272727
         [,257]     [,258]     [,259]     [,260]    [,261]     [,262]
[1,] 0.09090909 0.18181818 0.09090909 0.27272727 0.1818182 0.09090909
[2,] 0.18181818 0.09090909 0.27272727 0.09090909 0.3636364 0.18181818
[3,] 0.27272727 0.36363636 0.36363636 0.36363636 0.2727273 0.27272727
         [,263]     [,264]     [,265]     [,266]     [,267]    [,268]    [,269]
[1,] 0.09090909 0.09090909 0.09090909 0.09090909 0.09090909 0.2727273 0.4545455
[2,] 0.18181818 0.27272727 0.18181818 0.27272727 0.18181818 0.3636364 0.2727273
[3,] 0.27272727 0.18181818 0.27272727 0.18181818 0.27272727 0.1818182 0.1818182
         [,270]     [,271]     [,272]     [,273]     [,274]     [,275]
[1,] 0.36363636 0.09090909 0.09090909 0.36363636 0.09090909 0.09090909
[2,] 0.09090909 0.45454545 0.45454545 0.27272727 0.18181818 0.27272727
[3,] 0.27272727 0.18181818 0.36363636 0.09090909 0.27272727 0.18181818
         [,276]     [,277]     [,278]    [,279]     [,280]     [,281]
[1,] 0.09090909 0.27272727 0.09090909 0.1818182 0.09090909 0.09090909
[2,] 0.45454545 0.45454545 0.18181818 0.3636364 0.45454545 0.18181818
[3,] 0.27272727 0.09090909 0.27272727 0.4545455 0.18181818 0.27272727
         [,282]     [,283]     [,284]     [,285]     [,286]     [,287]
[1,] 0.09090909 0.09090909 0.09090909 0.09090909 0.27272727 0.09090909
[2,] 0.27272727 0.27272727 0.18181818 0.27272727 0.18181818 0.18181818
[3,] 0.36363636 0.18181818 0.27272727 0.18181818 0.09090909 0.27272727
         [,288]     [,289]     [,290]     [,291]     [,292]     [,293]
[1,] 0.27272727 0.09090909 0.09090909 0.18181818 0.45454545 0.09090909
[2,] 0.18181818 0.27272727 0.45454545 0.36363636 0.09090909 0.18181818
[3,] 0.09090909 0.18181818 0.27272727 0.09090909 0.27272727 0.36363636
         [,294]     [,295]    [,296]    [,297]    [,298]     [,299]     [,300]
[1,] 0.27272727 0.45454545 0.4545455 0.2727273 0.1818182 0.09090909 0.09090909
[2,] 0.36363636 0.27272727 0.2727273 0.1818182 0.2727273 0.27272727 0.45454545
[3,] 0.09090909 0.09090909 0.3636364 0.3636364 0.3636364 0.18181818 0.27272727
         [,301]     [,302]     [,303]    [,304]    [,305]     [,306]    [,307]
[1,] 0.09090909 0.09090909 0.09090909 0.4545455 0.1818182 0.27272727 0.2727273
[2,] 0.18181818 0.45454545 0.27272727 0.2727273 0.3636364 0.09090909 0.1818182
[3,] 0.27272727 0.27272727 0.36363636 0.1818182 0.4545455 0.18181818 0.3636364
         [,308]     [,309]    [,310]    [,311]     [,312]     [,313]     [,314]
[1,] 0.18181818 0.09090909 0.2727273 0.1818182 0.09090909 0.09090909 0.09090909
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