Statistical analysis for marker gene studies

Description

Compares the diversity or abundance between groups of samples using several ANOVA-type of analyses.

Parameters

Details

This tool takes two input files: a count table that contains the counts of the identified species or operational taxonomic units (OTUs) in each sample, and a phenodata table that specifies the grouping of the samples. Statistical tests only work for a dataset that contains 2-3 groups. The analyses are performed using the functionality offered by the R packages vegan, rich, biodiversityR, pegas and labdsv.

The tool produces rank abundance curves and rarefaction curves for all groups, and an RDA ordination plot.

Before running the RDA analysis, the species abundance values are standardized using the method specified by the parameter. The standardized values are also used for running the following ANOVA type of statistical analyses, which compare the diversity or abundance between the groups:

Contributed diversity analysis splits the observed "species" (taxa or OTUs) diversity to

Indicator species analysis using the Dufrene-Legendre method tries to find the "species" (taxa or OTUs) that have a high specificity to a single group. Indicator Species Analysis Minimizing Intermediate Occurrences calculates the degree of the species being present or absent in a certain group of samples.

Output

The analysis output consists of the following:

References

Consult the R packages vegan, rich, biodiversityR, pegas and labdsv for more details about the methods.