cMD

curatedMetagenomicData



Curated and processed metagenomic data through ExperimentHub

Getting Started

Installing curatedMetagenomicData should be done through the Bioconductor package manager biocLite(). Note that accessing the most recent datasets requires the development version of Bioconductor. Trying to install the development version of curatedMetagenomicData on top of the release version of Bioconductor won’t allow you to access datasets that have been added since the last Bioconductor release.

Install R and Bioconductor

To install the release version, follow instructions for installing R and Bioconductor from https://www.bioconductor.org/install/.

To install the development version, follow the instructions at http://bioconductor.org/developers/how-to/useDevel/.

If you’re not sure which version to use, look at the “Reference Manual” for the release and development versions.

Install curatedMetagenomicData

Through R/Bioconductor

This is the usual way to install curatedMetagenomicData and is preferred in most cases. You must have Bioconductor installed already.

library(BiocInstaller)
biocLite("curatedMetagenomicData")

If you are running the development version of Bioconductor, you can also install directly from Github for the “bleeding edge” version, which may contain bugs:

library(BiocInstaller)
biocLite("waldronlab/curatedMetagenomicData", dependencies = TRUE,
         build_vignettes = TRUE)

Accessing Data

From within R

curatedMetagenomicData and its related data can be accessed through R using Bioconductor and ExperimentHub.

The recommended way to access data from within R is with the curatedMetagenomicData() function. For example:

library(curatedMetagenomicData)
res <- curatedMetagenomicData("HMP_2012.metaphlan_bugs_list.stool", dryrun=FALSE) #one dataset
res <- curatedMetagenomicData("HMP_2012.metaphlan_bugs_list.*", dryrun=FALSE) #many datasets

See:

  • help(package="curatedMetagenomicData") for all datasets and available functions
  • ?curatedMetagenomicData for more options to this function, including whether to return relative abundances or counts, conversion of taxonomic tables to phyloseq objects, and versioning
  • ?combined_metadata or View(combined_metadata) for a table of all participants and their annotations. See the package vignette for additional instructions, and vignettes/extras for code to reproduce results of our manuscript.

Command line usage

Set up curatedMetagenomicData as above, then use the shell script provided in the inst/commandline package directory. This script generates tab-separated value files and takes similar arguments to the R function.