biom: An interface package (beta) for the BIOM file format.
Version 0.3.12

This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.

Browse man pages Browse package API and functions Browse package files

AuthorPaul J. McMurdie <mcmurdie@stanford.edu> and the biom-format team http://biom-format.org/
Date of publication2014-02-24 01:20:23
MaintainerPaul J. McMurdie <mcmurdie@stanford.edu>
LicenseGPL-2
Version0.3.12
URL https://github.com/joey711/biom/ http://biom-format.org/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("biom")

Man pages

biom-class: The biom format data class.
biom_data-methods: Access main data observation matrix data from 'biom-class'.
biom-methods: Build and return an instance of the biom-class.
biom-package: This is an R package for interfacing with the biom format.
biom_shape-methods: The matrix dimensions of a 'biom-class' object.
colnames-methods: Method extensions to 'colnames' for 'biom-class' objects.
header-methods: Extract the header from a 'biom-class' object as a list.
matrix_element_type-methods: Access class of data in the matrix elements of a 'biom-class'...
ncol-methods: Method extensions to 'ncol' for 'biom-class' objects.
nrow-methods: Method extensions to 'nrow' for 'biom-class' objects.
observation_metadata-methods: Access observation (row) meta data from 'biom-class'.
read_biom: Read a biom-format file, returning a 'biom-class'.
rownames-methods: Method extensions to 'rownames' for 'biom-class' objects.
sample_metadata-methods: Access meta data from 'biom-class'.
show-methods: Method extensions to show for biom objects.
write_biom: Write a biom-format file, returning a 'biom-class'.

Functions

biom Man page
biom,list-method Man page
biom-class Man page
biom-package Man page
biom_data Man page
biom_data,biom,ANY,character-method Man page
biom_data,biom,character,ANY-method Man page
biom_data,biom,missing,missing-method Man page
biom_data,biom,missing,numeric-method Man page
biom_data,biom,numeric,missing-method Man page
biom_data,biom,numeric,numeric-method Man page
biom_shape Man page
biom_shape,biom-method Man page
colnames Man page
colnames,biom-method Man page
header Man page
header,biom-method Man page
matrix_element_type Man page
matrix_element_type,biom-method Man page
ncol Man page
ncol,biom-method Man page
nrow Man page
nrow,biom-method Man page
observation_metadata Man page
observation_metadata,biom,character-method Man page
observation_metadata,biom,missing-method Man page
observation_metadata,biom,numeric-method Man page
read_biom Man page
rownames Man page
rownames,biom-method Man page
sample_metadata Man page
sample_metadata,biom,character-method Man page
sample_metadata,biom,missing-method Man page
sample_metadata,biom,numeric-method Man page
show Man page
show,biom-method Man page
write_biom Man page

Files

biom
biom/inst
biom/inst/tests
biom/inst/tests/test-accessors.R
biom/inst/tests/test-IO.R
biom/inst/NEWS
biom/inst/extdata
biom/inst/extdata/rich_dense_otu_table.biom
biom/inst/extdata/rich_dense_char.biom
biom/inst/extdata/rich_sparse_char.biom
biom/inst/extdata/min_sparse_otu_table.biom
biom/inst/extdata/rich_sparse_otu_table.biom
biom/inst/extdata/min_dense_otu_table.biom
biom/inst/doc
biom/inst/doc/biom-demo.R
biom/inst/doc/biom-demo.html
biom/inst/doc/placeholder.txt
biom/inst/doc/biom-demo.Rmd
biom/tests
biom/tests/testthat-biom.R
biom/NAMESPACE
biom/R
biom/R/BIOM-class.R
biom/R/IO-methods.R
biom/R/allClasses.R
biom/R/allPackage.R
biom/R/validity-methods.R
biom/vignettes
biom/vignettes/biom-demo.Rmd
biom/README.md
biom/MD5
biom/build
biom/build/vignette.rds
biom/DESCRIPTION
biom/man
biom/man/ncol-methods.Rd
biom/man/read_biom.Rd
biom/man/biom-package.Rd
biom/man/biom-methods.Rd
biom/man/biom_shape-methods.Rd
biom/man/nrow-methods.Rd
biom/man/biom-class.Rd
biom/man/observation_metadata-methods.Rd
biom/man/biom_data-methods.Rd
biom/man/sample_metadata-methods.Rd
biom/man/header-methods.Rd
biom/man/colnames-methods.Rd
biom/man/write_biom.Rd
biom/man/rownames-methods.Rd
biom/man/matrix_element_type-methods.Rd
biom/man/show-methods.Rd
biom documentation built on Jan. 15, 2017, 9:30 a.m.