|
 |
|
|
|
Frank
Delaglio, Ph.D.
Software Science Consultant
13840 Grey Colt Drive
North Potomac MD 20878 USA
Tel: 301 806-0867
Fax: 301 309-8717
E-mail: delaglio@nmrscience.com
|
|
|
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. |
|
Under Construction
|
[ Home ]
[ Terms of Use ]
[ Copyright ]
last updated: Jan 22, 2009 / big frank
Contact site designer mimi at
mdelaglio@hotmail.com
|
|
