biomformat: An interface package for the BIOM file format

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.

Author
Paul J. McMurdie <mcmurdie@stanford.edu> and Joseph N Paulson <jpaulson@jimmy.harvard.edu>
Date of publication
None
Maintainer
Paul J. McMurdie <mcmurdie@stanford.edu>
License
GPL-2
Version
1.2.0
URLs

View on Bioconductor

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'.

Files in this package

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