Read/Write, Transform, and Summarize 'BIOM' Data

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Documentation for package ‘rbiom’ version 1.0.3

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alpha.div Estimate the diversity of each sample.
beta.div Make a distance matrix of samples vs samples.
counts Get the abundance counts.
info Get biom's misc information.
metadata Get the sample metadata.
nsamples Number of samples in a BIOM.
ntaxa Number of taxa in a BIOM.
phylogeny Get the phylogenetic tree.
print Summarize the contents of a BIOM object
print.BIOM Summarize the contents of a BIOM object
rarefy Subset counts so that all samples have the same number of observations.
rbiom rbiom: Read/Write, Transform, and Summarize BIOM Data
read.biom Extracts counts, metadata, taxonomy, and phylogeny from a biom file.
read.fasta Parse a fasta file into a named character vector.
read.tree Read a newick formatted phylogenetic tree.
sample.names Get the sample names.
select Reduce samples to a specific list
sequences DNA sequence associated with each taxonomic identifier.
subset Subset samples using the BIOM object's metadata
subset.BIOM Subset samples using the BIOM object's metadata
subtree Create a subtree by specifying tips to keep.
taxa.names Get the taxa names.
taxa.ranks Get the taxa ranks.
taxa.rollup Generate a matrix of samples by taxa, at the specified taxonomic rank.
taxonomy Get the taxonomy table.
tips Names of a phylogenetic tree's tips/leafs.
unifrac Compute Weighted and Unweighted UniFrac distance matrices.
write.biom Write counts, metadata, taxonomy, and phylogeny to a biom file.
write.fasta Write sequences from a BIOM object to a file in fasta format.
write.tree Write a newick formatted phylogenetic tree.
write.xlsx Write data and summary information to a Microsoft Excel-compatible workbook.