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 477 9.88996 9.18445 9.54911 9.5817 10.2308 9.40279 ...
0.03 F3D1 477 9.60907 9.43451 8.71598 7.15374 7.34357 8.02411 ...
0.03 F3D141 477 9.95792 9.74602 9.59162 10.2709 10.0893 9.48213 ...
0.03 F3D142 477 9.63123 9.71172 8.85024 8.94842 9.68349 9.2929 ...
0.03 F3D143 477 9.31475 9.00044 9.18714 9.446 10.0193 9.26821 ...
0.03 F3D144 477 9.94975 9.43993 9.53749 9.8189 10.3886 9.65467 ...
0.03 F3D145 477 10.3498 10.0028 10.0537 10.2468 10.5823 10.084...
0.03 F3D146 477 9.2422 8.83781 8.97917 9.67714 9.79838 9.17101 ...
0.03 F3D147 477 10.8948 10.6442 10.2095 10.5707 11.1926 10.5693 ...
0.03 F3D148 477 10.2892 10.1178 9.76077 10.4354 11.0028 10.24023 ...
0.03 F3D149 477 10.2242 10.0888 9.97982 10.3854 10.4152 9.98204 ...
0.03 F3D150 477 9.21106 8.8547 9.58328 9.9294 9.29564 9.26974 ...
0.03 F3D2 477 12.0676 10.9716 10.5374 9.29773 7.6902 9.16022 ...
0.03 F3D3 477 11.341 10.7271 10.2862 9.18923 6.16589 9.3770 ...
0.03 F3D5 477 9.49838 9.25596 9.26208 8.58889 5.70137 8.47747 ...
0.03 F3D6 477 10.8964 10.3273 10.0652 9.65305 4.66436 9.55513 ...
0.03 F3D7 477 10.8735 10.5142 10.2923 9.90326 4.87351 9.5801 ...
0.03 F3D8 477 9.02401 9.41283 9.34594 8.14137 2.14137 8.58432 ...
0.03 F3D9 477 9.71762 9.49965 9.69759 8.51499 3.27468 8.94711 ...
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
0.1.
mothur > make.clr(shared=final.opti_mcc.shared, zero=0.01)
Revisions
- 1.44.0 - First Introduced. #695