phyloseq package provides many functions for exploring and visualising metagenomics data and we will work through two of the vignettes provided by the package authors today.
A copy of the R source code from the vignettes is available to you in the
labs/5_Friday foler, so you can retrace the steps shown in the vignettes.
To find out more about the packge, have a look at the package landing page on the Bioconductor website.
If we don’t have the appropriate packages intalled yet, we will do so now from the local repository (At home we can just use
biocLite to install those).
source("http://192.168.0.9/setRepos.R") install.packages(c("phyloseq", "metagenomeSeq"))
We can have a look at available vignettes by running the followign command:
vignette(package = "phyloseq")
I suggest that we go through the “Phyloseq-Analysis” vignette first, since it allows for a direct “hands-on” exploration of the things we can do with the
A .pdf copy of the paper correspoding to the
GlobalPatterns example dataset is provided in the course materials today, it is referenced in the vignette from time to time and you can use it to compare your plots with the plots from the paper.
As a second step we can work through the
phyloseq-mixture-models vignette from the
phyloseq paper, which will give us an introduction on how to use