make.clr
The make.clr command converts a shared file to a centered log ratio file. The make.clr command parameters are shared, groups, zero and label. The shared file is required.
Default Settings
The shared file is required.
mothur > make.clr(shared=final.opti_mcc.shared)
The clr file will look like:
label Group numOtus Otu001 Otu002 Otu003 Otu004 Otu005 Otu006 ...
0.03 F3D0 531 5.41759 4.92983 5.18186 5.20439 5.65345 5.08071 ...
0.03 F3D1 531 5.14707 5.02644 4.53046 3.45783 3.5875 4.05412 ...
0.03 F3D141 531 5.34869 5.20222 5.09554 5.56513 5.43955 5.0199 ...
0.03 F3D142 531 5.0383 5.09387 4.49989 4.56748 5.07438 4.8049 ...
0.03 F3D143 531 4.78115 4.56456 4.69318 4.87166 5.26746 4.74906 ...
0.03 F3D144 531 5.33322 4.98106 5.04841 5.24279 5.63662 5.12934 ...
0.03 F3D145 531 5.71435 5.47431 5.50955 5.64309 5.87528 5.53097...
0.03 F3D146 531 4.93426 4.65515 4.75268 5.24294 5.31859 4.8851 ...
0.03 F3D147 531 6.27643 6.10363 5.80262 6.05272 6.4835 6.05177 ...
0.03 F3D148 531 5.78974 5.67112 5.42408 5.89096 6.28392 5.755883 ...
0.03 F3D149 531 5.75472 5.66097 5.58554 5.86629 5.88696 5.58708 ...
0.03 F3D150 531 4.90698 4.66102 5.16412 5.40341 4.96539 4.9475 ...
0.03 F3D2 531 7.02949 6.27018 5.96945 5.11146 4.00172 5.01637 ...
0.03 F3D3 531 6.18414 5.75926 5.45427 4.69675 2.63837 4.82629 ...
0.03 F3D5 531 5.0131 4.84572 4.84995 4.38584 2.42641 4.30915 ...
0.03 F3D6 531 6.07615 5.68224 5.50091 5.21585 1.83537 5.14816 ...
0.03 F3D7 531 5.85551 5.60691 5.4535 5.18464 1.80025 4.9615 ...
0.03 F3D8 531 4.77529 5.0438 4.99759 4.16704 0.405839 4.47201 ...
0.03 F3D9 531 5.29494 5.14422 5.28108 4.46432 1.00905 4.76247 ...
Options
groups
The groups parameter allows you to specify which of the groups in your sharedfile you would like included. The group names are separated by dashes.
mothur > make.clr(shared=final.opti_mcc.shared, groups=F3D7-F3D8-F3D9)
label
The label parameter allows you to select what distance levels you would like, and are also separated by dashes.
mothur > make.clr(shared=final.opti_mcc.shared, label=0.03)
zero
The zero parameter allows you to set an value for zero OTUs. Default is 1.
mothur > make.clr(shared=final.opti_mcc.shared, zero=0.01)
Revisions
- 1.48.2 Updates to clr value calculation.
- 1.44.0 - First Introduced. #695