The GeneCycle Package - NexTag Supports Open Source Initiatives

More documents

Recommendations

Info

10 robust.g.testArgumentsyxDetailsValueindexthe matrix consisting of the spectral estimates as column vectorsa matrix consisting of the time series as column vectors. In robust.g.testonly needed if permutation tests are usedan index to the spectral estimates that is to be used in the testing for periodicity.If index is missing, the maximum component of the spectral estimate is usedin testing (regardless of the frequency of this maximum)permif perm is FALSE, a simulated distribution for the g-statistic is used. If perperm is TRUE, permutation tests are used to find the distribution of the g-statistic for each time series separately.noOfPermutationsnumber of permutations that are used for each time series (default = 5000)Application of robust.g.test can be very computer intensive, especially the production of thedistribution of the test statistics may take a lot of time. Therefore, this distribution (dependeningon the length of the time series) is stored in an external file to avoid recomputation (see examplebelow).For the general idea behind the Fisher’s g test also see fisher.g.test which implements ananalytic approach for g-testing. This is faster but not robust and also assumes Gaussian noise.robust.g.test returns a list of p-values, and g.statistic the associated test statistics.robust.spectrum returns a matrix where the column vectors correspond to the spectra correspondingto each time series.Author(s)Miika Ahdesmaki (〈miika.ahdesmaki@tut.fi〉).ReferencesFisher, R.A. (1929). Tests of significance in harmonic analysis. Proc. Roy. Soc. A, 125, 54–59.Ahdesmaki, M., Lahdesmaki, H., Peason, R., Huttunen, H., and Yli-Harja O. (2005). BMC Bioinformatics6:117.See Alsofdrtool, fisher.g.test.Examples## Not run:# load GeneCycle librarylibrary("GeneCycle")
obust.g.test 11# load data setdata(caulobacter)# how many samples and and how many genes?dim(caulobacter)# robust, rank-based spectral estimator applied to first 5 genesspe5
Page 1 and 2: The GeneCycle PackageFebruary 16, 2
Page 3 and 4: avpg 3ValueA list object with the f
Page 5 and 6: dominant.freqs 5dominant.freqsDomin
Page 7 and 8: is.constant 7See Alsofdrtool.Exampl
Page 9: obust.g.test 9freqA vector with fre

The GeneCycle Package - NexTag Supports Open Source Initiatives

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?