In this folder there are 4 main files for period identification of circadian transcripts measured with microarray technology.

1)'periodEstimateMARepWT' is used when no pseudo-sinusoidal waves are required and two replicates are available for each transcript time series
2)'periodEstimateMAWT' is used when no pseudo-sinusoidal waves are required and only one replicate is available for each transcript time series
3)'periodEstimateMARep' is used when pseudo-sinusoidal waves are required and two replicates are available for each transcript time series
4)'periodEstimateMA' is used when pseudo-sinusoidal waves are required and only one replicate is available for each transcript time series

The syntax for the code 1) and 3) is:

[Period, Amp, Phase, class, Pihat]=periodEstimateMARepWT(data1,data2,fs,Min,Max,varargin)
and
[Period, Amp, Phase, class, Pihat]=periodEstimateMARep(data1,data2,fs,Min,Max,varargin)

'data1' and 'data2' are the two replicates of the transcript time series (input as row vectors); fs is the sampling frequency of the time series;
'Min' and 'Max' are the minimum and the maximum period considered; 
'varargin' includes extra inputs for graphical display:
varargin{1}=0/1 if plotting is of interest (1) or not (0). 0 is default
varargin{2}=Name of the signal for plot title
varargin{3}=Number of the signal in the array (add to the Name in the line above to form the title of the figure).
varargin{4}=Starting time of the experiment, if that's not zero. For instance, if data has bee collected started at ZT24, then type '24' in this entry

The code returns Period, Amplitude (Amp), and Phase of the signal. Phase is computed using a cosine function as base. 
Pihat is the logit probability that the signal is periodic.

The syntax for code 2) and 4) is:

[Period, Amp, Phase, Pihat]=periodEstimateMAWT(data,fs,Min,Max,varargin)
and
[Period, Amp, Phase, Pihat, class]=periodEstimateMA(data,fs,Min,Max,varargin)

The inputs are identical as in the multiple repeat case, with the exception that only 1 replicate is expected.
The outputs of 'periodEstimateMAWT' are the same as before, while the output for 'periodEstimateMA' include 'class' which returns which pseudo-sinusoid
was used (1 is standard sinusoid, while 2 and 3 are define in the program as in the paper).

NOTE: To analyse data that needs detrending, uncomment line 18 and 22 in code 2) and 4), and 45 and 41 in code 1) and 3)