Man pages for rbiom
Read/Write, Transform, and Summarize 'BIOM' Data
| 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. |
| pipe | Pipe operator |
| Summarize the contents of a BIOM object | |
| rarefy | Subset counts so that all samples have the same number of... |
| rbiom | rbiom: Read/Write, Transform, and Summarize BIOM Data |
| read.biom | Extracts counts, metadata, taxonomy, and phylogeny from a... |
| 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 |
| 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... |
| 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... |
| 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... |
