aq-mrpp.1

.\" Authors: Andre Masella
.TH aq-mrpp 1 "May 2013" "1.6" "USER COMMANDS"
.SH NAME 
aq-mrpp \- Compute Multi Response Permutation Procedure of within- versus among-group dissimilarities in R
.SH SYNOPSIS
.B aq-mrpp -i otu_table -m mapping.txt -d distance_method -o output_dir
.SH DESCRIPTION
Multiple Response Permutation Procedure (MRPP) provides a test of whether there is a significant difference between two or more groups of samples. Samples are group based on all provided variables from the \fBmapping.txt\fR file. For each variable, three plots are produced: a multi-dimensional scaling, histogram of the differences among groups, and a graph of mean distances. This is done using the \fBvegan\fR R package. Options for method are: "manhattan", "euclidean", "canberra", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup", "binomial", "chao" or "cao". Recommended method is "bray", which uses Bray-Curtis distances to create the plots. OTU table must be provided in tab delimited format.

Outputs an NMDS plot in PDF form, and various MRPP statistics (A value, stress value, etc.) in text file format.
.SH SEE ALSO
.BR axiome (1).