This package is a toolkit for working with Biological Observation Matrix (BIOM) files. Features include reading/writing all BIOM formats, rarefaction, alpha diversity, beta diversity (including UniFrac), summarizing counts by taxonomic level, and sample subsetting. Standalone functions for reading, writing, and subsetting phylogenetic trees are also provided. All CPU intensive operations are encoded in C with multi-thread support.
Reference material is available online at https://cmmr.github.io/rbiom/index.html
Source code can be found at https://github.com/cmmr/rbiom
The latest stable version can be downloaded from CRAN.
The development version is available on GitHub.
library(rbiom) infile <- system.file("extdata", "hmp50.bz2", package = "rbiom") biom <- read.biom(infile) # Rarefy to 1000 reads per sample biom <- rarefy(biom, depth=1000) # Summarize counts by phylum phyla <- taxa.rollup(biom, 'Phylum') phyla[1:4,1:6] # Work with metadata table(biom$metadata$Sex, biom$metadata$Body.Site) sprintf("Mean age: %.1f", mean(biom$metadata$Age)) # Draw the phylogenetic tree plot(biom$phylogeny) # Get unifrac distance matrix dm <- beta.div(biom, 'unifrac')
Several functions will by default use all available CPU cores. To limit the number of cores used, you can set the numThreads option:
RcppParallel::setThreadOptions(numThreads = 4)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.