added make.lefse command. fixed bug in make.contigs with trimming reverse barcodes...

[mothur.git] / lefsecommand.h

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+//
+//  lefsecommand.h
+//  Mothur
+//
+//  Created by SarahsWork on 6/12/13.
+//  Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#ifndef __Mothur__lefsecommand__
+#define __Mothur__lefsecommand__
+
+#include "command.hpp"
+
+/* 
+ Columns = groups, rows are OTUs, class = design??
+ 
+ From http://huttenhower.sph.harvard.edu/galaxy/root?tool_id=lefse_upload
+ Input data consist of a collection of m samples (columns) each made up of n numerical features (rows, typically normalized per-sample, red representing high values and green low). These samples are labeled with a class (taking two or more possible values) that represents the main biological hypothesis under investigation; they may also have one or more subclass labels reflecting within-class groupings.
+ 
+ Step 1: the Kruskall-Wallis test analyzes all features, testing whether the values in different classes are differentially distributed. Features violating the null hypothesis are further analyzed in Step 2.
+ Step 2: the pairwise Wilcoxon test checks whether all pairwise comparisons between subclasses within different classes significantly agree with the class level trend.
+ Step 3: the resulting subset of vectors is used to build a Linear Discriminant Analysis model from which the relative difference among classes is used to rank the features. The final output thus consists of a list of features that are discriminative with respect to the classes, consistent with the subclass grouping within classes, and ranked according to the effect size with which they differentiate classes.
+*/
+
+#endif /* defined(__Mothur__lefsecommand__) */