biomformat: An interface package for the BIOM file format
Version 1.4.0

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 Joseph N Paulson <jpaulson@jimmy.harvard.edu>
Bioconductor views DataImport Metagenomics Microbiome
Date of publicationNone
MaintainerPaul J. McMurdie <mcmurdie@stanford.edu>
LicenseGPL-2
Version1.4.0
URL https://github.com/joey711/biomformat/ http://biom-format.org/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("biomformat")

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.
make_biom: Create a 'biom-class' from 'matrix-class' or 'data.frame'.
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'.
read_hdf5_biom: Read in a biom-format vs 2 file, returning a 'list'.
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 v1 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,biom-method Man page
extract_metadata Source code
generate_matrix Source code
generate_metadata Source code
header Man page
header,biom-method Man page
make_biom Man page Source code
matrix_element_type Man page
matrix_element_type,biom-method Man page
namedList Source code
ncol,biom-method 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 Source code
read_hdf5_biom Man page Source code
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,biom-method Man page
validbiom Source code
write_biom Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/BIOM-class.R
R/IO-methods.R
R/allClasses.R
R/allPackage.R
R/validity-methods.R
README.md
build
build/vignette.rds
inst
inst/doc
inst/doc/biomformat.R
inst/doc/biomformat.Rmd
inst/doc/biomformat.html
inst/extdata
inst/extdata/min_dense_otu_table.biom
inst/extdata/min_sparse_otu_table.biom
inst/extdata/min_sparse_otu_table_hdf5.biom
inst/extdata/rich_dense_char.biom
inst/extdata/rich_dense_otu_table.biom
inst/extdata/rich_sparse_char.biom
inst/extdata/rich_sparse_otu_table.biom
inst/extdata/rich_sparse_otu_table_hdf5.biom
man
man/biom-class.Rd
man/biom-methods.Rd
man/biom-package.Rd
man/biom_data-methods.Rd
man/biom_shape-methods.Rd
man/colnames-methods.Rd
man/header-methods.Rd
man/make_biom.Rd
man/matrix_element_type-methods.Rd
man/ncol-methods.Rd
man/nrow-methods.Rd
man/observation_metadata-methods.Rd
man/read_biom.Rd
man/read_hdf5_biom.Rd
man/rownames-methods.Rd
man/sample_metadata-methods.Rd
man/show-methods.Rd
man/write_biom.Rd
tests
tests/testthat
tests/testthat-biomformat.R
tests/testthat/test-IO.R
tests/testthat/test-accessors.R
vignettes
vignettes/biomformat.Rmd
biomformat documentation built on May 20, 2017, 10:40 p.m.