This repository contains the code described in Hutchison, Maienschein-Cline, and Chiang et al. (2015) Improved statistical methods enable greater sensitivity in rhythm detection for genome-wide data. PLoS Comput Biol 11(3): e1004094. doi:10.1371/journal.pcbi.1004094
Hi Alan,
I am new to using tools to find rhythmicity in datasets from gut microbiota.
I have read Hutchison et al . 2015 PLOS Computation Biology and Leone et al. 2015 Cell Host and Microbes.
I understand that now the eJTK in addition to the empirically calculated the p-values provides another p-value by using the Gamma distribution based on 1000 permutations.
However, I had some basic queries with the using eJTK;
(a). Is it that in the current version of eJTK, the default waveform used is cosine and with the help of "asymmetry" flag we can account for other possible waveforms (other than sinusoidal)?
(b). Is there any criteria I should look for which will help in choosing the steps for "phase" and "asymmetry" search (a phase search every 2 hr from ZT0 to ZT22 vs.every 4 hr from ZT0 to ZT20?
(c). Does the sampling frequency (2hr/4hr/6hr) guide the criteria for "phase" and "asymmetry" search ?
Hi Alan, I am new to using tools to find rhythmicity in datasets from gut microbiota. I have read Hutchison et al . 2015 PLOS Computation Biology and Leone et al. 2015 Cell Host and Microbes. I understand that now the eJTK in addition to the empirically calculated the p-values provides another p-value by using the Gamma distribution based on 1000 permutations.
However, I had some basic queries with the using eJTK; (a). Is it that in the current version of eJTK, the default waveform used is cosine and with the help of "asymmetry" flag we can account for other possible waveforms (other than sinusoidal)? (b). Is there any criteria I should look for which will help in choosing the steps for "phase" and "asymmetry" search (a phase search every 2 hr from ZT0 to ZT22 vs.every 4 hr from ZT0 to ZT20? (c). Does the sampling frequency (2hr/4hr/6hr) guide the criteria for "phase" and "asymmetry" search ?
Thank you, Shrez