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Lefse

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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.

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