lefse
The lefse command is modeled after the LEfSe program written and published by the Huttenhower lab. See make.lefse for formating files for input into the original LEfSe program.
Default Setting
The shared and design parameters are required.
mothur > lefse(shared=final.an.shared, design=mouse.sex_time2.design)
If you open the final.an.0.03.lefse_summary file, you will see:
OTU LogMaxMean Class LDA pValue
Otu001 5.21329 -
Otu002 5.06449 -
Otu003 5.08958 -
Otu004 5.06121 -
Otu005 4.82611 -
Otu006 4.76942 -
Otu007 4.81303 -
Otu008 4.69046 -
Otu009 4.71183 -
Otu010 4.77212 -
Otu011 4.63326 -
Otu012 4.80072 F003Late 4.43296 0.0363836
Otu013 4.58877 F003Late 4.02028 0.0363836
Otu014 4.5691 -
Otu015 4.42951 -
...
Options
class
The class parameter is used to indicate the which category you would like used as the class. If none is provided first category is used.
subclass
The subclass parameter is used to indicate the which category you would like used as the subclass. If none is provided the class is used.
sets
The sets parameter allows you to specify which of the sets in your design file you would like to analyze. The set names are separated by dashes. The default is all sets in the designfile.
label
The label parameter is used to indicate which distances in the shared file you would like to use. labels are separated by dashes.
pairwise
The pairwise parameter allows you to run all pairwise comparisons of the sets in your design file. Default=f.
walpha
The walpha parameter is used to set the alpha value for the Wilcoxon test. Default=0.05.
aalpha
The aalpha parameter is used to set the alpha value for the Krukal Wallis Anova test Default=0.05.
lda
The lda parameter is used to set the threshold on the absolute value of the logarithmic LDA score. Default=2.0.
wilc
The wilc parameter is used to indicate whether to perform the Wilcoxon test. Default=T.
iters
The iters parameter is used to set the number of bootstrap iteration for LDA. Default=30.
curv
The curv parameter is used to set whether perform the wilcoxon testing the Curtis’s approach [beta version] Default=F.
fboots
The fboots parameter is used to set the subsampling fraction value for each bootstrap iteration. Default=0.67.
strict
The strict parameter is used to set the multiple testing correction options. 0 no correction (more strict, default), 1 correction for independent comparisons, 2 correction for independent comparison. Options = 0,1,2. Default=0.
minc
The minc parameter is used to minimum number of samples per subclass for performing wilcoxon test. Default=10.
multiclass
The multiclass parameter is used to (for multiclass tasks) set whether the test is performed in a one-against-one ( onevone - more strict!) or in a one-against-all setting ( onevall - less strict). Default=onevall.
norm
The norm parameter is used to multiply relative abundances by 1000000. Recommended when very low values are present. Default=T.
Revisions
- 1.32.0 - First Introduced
- 1.37.0 - Fixes “Skipping x iter...” warning.
- 1.38.0 - Adds sets parameter
- 1.40.0 - Speed and memory improvements for shared files. #357 , #347
- 1.40.0 Bug Fix: Fixes seeded random issue. #416
- 1.45.0 Fixes lefse screen output.
- 1.46.0 Adds pairwise parameter. #781
- 1.47.0 Forces lefse pairwise comparisons.
- 1.48.0 Fixes bug with sets parameter not passing to pairwise lefse calc