Help for 'components' program.

Date help created:  25 Sep 2000
Date last updated:  25 Sep 2000
'components' calculates the principal components of a group of spectra. The pseudo-spectra, which are the linear combinations of the spectra as determined by the compnents, can be output, as well as the weights of each spectrum relative to the components.

The input data files must not be deflated.

To run the program type

	components <components script file>

The components script file must have the following format:

	input_list  <file containing list of input par files>
	output_data <prefix for output pseudo-spectra> ! optional
	output_weights <output weights file> ! optional
	components <minimum number of components to calculate> ! optional
	fraction <minimum fraction of weight to calculate> ! optional
	correlation ! optional

One or both of 'output_data' and 'output_weights' must be given.

The input list file must have just a list of files, one per line.

The minimum number of components calculated is 1/10 the number of input files if 'components' does not appear.

The minimum fraction of weight (the sum of the eigenvalues) calculated is 0.95 if 'fraction' does not appear.

If 'correlation' appears the correlation matrix is used to calculate the principal components, otherwise the covariance matrix is used. The correlation matrix is basically the normalised covariance matrix. In general, it is probably best to use the covariance matrix.

The following is an example script file:

	input_list 84list.txt
	output_data 84pca.spc
	output_weights 84weights.txt
	components 4
	fraction 0.9

with 84list.txt being:

	841.spc.par
	842.spc.par
	843.spc.par
	844.spc.par
	845.spc.par
	846.spc.par
	847.spc.par
	848.spc.par

Assuming the first 4 components are sufficient to give 0.9 of the total weight then the following files are created because of the 'output_data' statement:

	84pca.spc1
	84pca.spc2
	84pca.spc3
	84pca.spc4

The corresponding par files are also created:

	84pca.spc1.par
	84pca.spc2.par
	84pca.spc3.par
	84pca.spc4.par

Azara help: components / W. Boucher / azara@bioc.cam.ac.uk