taxa.rollup: Generate a matrix of samples by taxa, at the specified...
In rbiom: Read/Write, Transform, and Summarize 'BIOM' Data

Description Usage Arguments Value Examples

Generate a matrix of samples by taxa, at the specified taxonomic rank.

1	taxa.rollup(biom, rank = "OTU", map = NULL, lineage = FALSE, sparse = FALSE)

`biom`	A `matrix`, `simple_triplet_matrix`, or `BIOM` object, as returned from read.biom. For matrices, the rows and columns are assumed to be the taxa and samples, respectively.
`rank`	The taxonomic rank. E.g. “OTU”, “Phylum”, etc. May also be given numerically: 0 for OTU, 1 for the highest level (i.e. Kingdom), and extending to the number of taxonomic ranks encoded in the original biom file. See example below to fetch the names of all available ranks.
`map`	A character matrix defining the value that each taxa IDs is assigned for each taxonomic rank. If `map=NULL` and `biom` is a `BIOM` class object, the map will be automatically loaded from `biom$taxonomy`. `map` must not be `null` when `biom` is a `matrix` or `simple_triplet_matrix`. See the example below for an example of `map`'s structure.
`lineage`	Include all ranks in the name of the taxa. For instance, setting to `TRUE` will produce `Bacteria; Actinobacteria; Coriobacteriia; Coriobacteriales`. Whereas setting to `FALSE` (the default) will return simply `Coriobacteriales`. You want to set this to TRUE if you have genus names (such as Incertae_Sedis) that map to multiple higher level ranks.
`sparse`	If true, returns a sparse matrix as described by `slam::simple_triplet_matrix`, otherwise returns a normal R matrix object. Sparse matrices will likely be considerably more memory efficient in this scenario.

A numeric matrix with samples as column names, and taxonomic identifiers as row names.

    library(rbiom)
    
    infile <- system.file("extdata", "hmp50.bz2", package = "rbiom")
    biom <- read.biom(infile)
    
    colnames(biom$taxonomy)
    
    phyla <- taxa.rollup(biom, 'Phylum')
    phyla[1:4,1:6]
    
    # Custom matrices should be formatted like so:
    counts <- as.matrix(biom$counts)
    map    <- biom$taxonomy
    
    counts[1:3,1:6]
    map[1:3,1:4]
    
    phyla <- taxa.rollup(counts, 'Phylum', map=map)
    phyla[1:3,1:6]