Using RDPTools Output with R/Bioconductor package Phyloseq
Follow this tutorial to use command-line RDPTools (Cole et al., 2014) and import results into the R/Bioconductor package phyloseq (McMurdie and Holmes, 2012). Use customized vignette to populate a phyloseq object with an OTU table, sample data table, classification table, tree file, and reference sequences. Once this is done, the data can be analyzed not only using phyloseq's wrapper functions, but by any method available in R. Detailed examples of analysis are provided with sample data file, example commands, output files and R plots, such as Abundance plot, Heatmap, Alpha Diversity Measurement plot, Cluster Dendrogram and Ordination (NMDS, PCA).
- Generating Cluster Output (Unsupervised Method)
- Generating Classifier Output (Supervised Method)
- Examples of Data Analysis