Package matR (Metagenomics Analysis Tools for R) is an analysis client for the
MG-RAST metagenome annotation engine, part of the US Department of Energy (DOE)
Systems Biology Knowledge Base (KBase). Customized analysis and visualization
tools securely access remote data and metadata within the popular open source R
language and environment for statistical computing.
See: http://mg-rast.org
CRAN (Comprehensive R Archive Network) hosts the package.
During an R session, load matR with:
> library(matR)
> remove.packages('matR') # if necessary
> install.packages('devtools')
> library(devtools)
> install_github(repo='MG-RAST/matR') > library(matR)
> dependencies()
> # auth.MGRAST('MgRastWebKeyGoesHereKEJ88') # get this from the upload page if you need to access private data
> list_mgp80869 <- metadata("mgp80869")$mgp80869 # Cross CZO soil depth profiles project
> biom_phylum <- biomRequest(list_mgp80869, request="organism", hit_type="all", source="RDP", group_level="phylum", evalue=15, wait=TRUE)
> phylum_matrix <- as.matrix(biom_phylum)
> dimnames(phylum_matrix)