Programs of the NMRPipe System
pcaNMR: Principal Component Analysis PCA Decomposition of Regions in NMRPipe-format Data

Flag Argument Default Description
 -in inName ... Input Name, Template, or List.
 -reg regList Full Point Coords of Region for PCA. Requires -in option.
 -nc numComp 4 Number of Components. (Use Zero for Auto)
 -itmax itmax 50 Max Iterations Per Component.
 -conv cTol 1e-6 Convergence Tolerance.
 -noverb No Verbose Mode Off.
Initial Conditions for Iteration:
 -avg Use Average Vector.
 -proj Use Projection.
 -maxvec Use Vector with Max Height.
 -first Use First Vector (Default) Also: -noavg.
Scaling Options:
 -center Use Mean-centering.
 -scale Use Variance Scaling.
 -autoScale Use Both Centering and Scaling.
 -autoScale Use Both Centering and Scaling.
 -mask maskName 2D Mask File.
Residual Test for Rank Estimation and Auto Component Count:
 -rank Do Initial Rank Estimation.
 -extra numExtra 0 Extra Components.
 -noise nDev 0.0 RMS Noise Estimate.
 -confid cProb 0.95 Confidence Limit.
 -thresh tHi 0.0 Detection Threshold.
Residual Test Method (Choose Only One):
 -nores No Residual Test (Default).
 -maxres Test by Maximum Residual. Requires -thresh flag.
 -expl Test explained var.
 -maxchi Test both Maximum Residual and Chi-Square. Requires -noise flag.
 -chi Test by Chi-Square. Requires -noise flag.
Output Files:
 -pca pcaTemplate Save Components.
 -res resTemplate Save Residuals.
 -score scoreName Save Score Vectors.
 -load loadName Save Load Vectors.

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