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.

AuthorPaul J. McMurdie <mcmurdie@stanford.edu> and Joseph N Paulson <jpaulson@jimmy.harvard.edu>
Date of publicationNone
MaintainerPaul J. McMurdie <mcmurdie@stanford.edu>
LicenseGPL-2
Version1.2.0
https://github.com/joey711/biomformat/
http://biom-format.org/

View on Bioconductor

Functions

biom Man page
biom-class 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,list-method Man page
biom-package Man page
biom_shape Man page
biom_shape,biom-method Man page
colnames,biom-method Man page
header Man page
header,biom-method Man page
make_biom Man page
matrix_element_type Man page
matrix_element_type,biom-method Man page
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
read_hdf5_biom 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,biom-method Man page
write_biom Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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