biomformat v1.0.2

by Paul McMurdie

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.

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The biomformat Package for R

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About

This is an R package for interfacing with both the JSON and HDF5 versions of the biom file format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file.

Design

The design of this API is intended to match the python API where appropriate, while maintaining 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.

Installation

To install the latest stable release of the biomformat package enter the following in an R session (after official release).

source("http://bioconductor.org/biocLite.R")
biocLite("biomformat")

Before official release, or to install the latest development version, enter the following into an R session.

install.packages("devtools") # if not already installed
devtools::install_github("joey711/biomformat")

Support

  • Please post feature or support requests and bugs at the Issues Tracker for the biomformat package on GitHub. Issues related to the format itself and not the R interface should be posted on the issues tracker for the biom-format team.

  • Note that this is a separate (but friendly!) project from the biom-format team, and the software license is different between this package and much of the rest of the biom-format software, which has switched to BSD.

  • This package is scheduled for inclusion in the next stable release of the Bioconductor project (BioC). BioC is also where the rhdf5 package lives.

  • The original release of this package was made available through CRAN, as the "biom" package, supporting version 1.x (JSON) only. The current plan is to let "biom" remain on CRAN in maintenance-only mode until "biomformat" is released on Bioconductor. At which point "biom" will be considered deprecated, and eventually removed.

Functions in biomformat

Name Description
biom-package This is an R package for interfacing with the biom format.
colnames,biom-method Method extensions to colnames for biom-class objects.
show,biom-method Method extensions to show for biom objects.
write_biom Write a biom-format v1 file, returning a biom-class.
make_biom Create a biom-class from matrix-class or data.frame.
header Extract the header from a biom-class object as a list.
nrow,biom-method Method extensions to nrow for biom-class objects.
observation_metadata Access observation (row) meta data from biom-class.
biom-class The biom format data class.
biom Build and return an instance of the biom-class.
matrix_element_type Access class of data in the matrix elements of a biom-class object
biom_data Access main data observation matrix data from biom-class.
biom_shape The matrix dimensions of a biom-class object.
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.
ncol,biom-method Method extensions to ncol for biom-class objects.
rownames,biom-method Method extensions to rownames for biom-class objects.
sample_metadata Access meta data from biom-class.
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Details

Date 2016-04-16
License GPL-2
Type Package
BugReports https://github.com/joey711/biomformat/issues
URL https://github.com/joey711/biomformat/, http://biom-format.org/
VignetteBuilder knitr
Collate 'allClasses.R' 'allPackage.R' 'IO-methods.R' 'BIOM-class.R' 'validity-methods.R'
biocViews DataImport, Metagenomics, Microbiome
NeedsCompilation no

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