The beta-diversity of ARGs was ordinated by principal coordinate analysis (PCoA) (R function “ordinate”, R-package “phyloseq” (McMurdie and Holmes, 2013)) based on Bray-Curtis distance. Permutational multivariate analysis (R function “adonis”, R-package “vegan” ( Dixon, 2003 ) was performed to test the differences in beta-diversity between groups.
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Further bioinformatics was performed with the phyloseq package in R.3.2.2.Results: Data on 291 sequenced BALs from 50 controls (mean age 6.1 years) and 106 CFs (mean age 3.6 years) shows the CF lower airway microbiome is distinct from the non-CF, has lower diversity, and different relative abundance at phylum, family and genus level.
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Dec 23, 2020 · x: phyloseq-class object. type 'OTU' or 'TAXONOMY' or 'METADATA' path: Path to the directory/folder where the data will be written. Uses the working directory by default.
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Jun 24, 2016 · Like PCoA and DPCoA, this method can be run using ordinate in phyloseq. In order to use supplemental sample data, it is necessary to provide an extra argument, specifying which of the features to consider – otherwise, phyloseq defaults to using all sample_data measurements when producing the ordination.
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compare_categories.py – Analyzes statistical significance of sample groupings using distance matrices¶. Description: This script allows for the analysis of the strength and statistical significance of sample groupings using a distance matrix as the primary input.