Package: biomformat 1.35.0

Paul J. McMurdie

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.

Authors:Paul J. McMurdie <[email protected]> and Joseph N Paulson <[email protected]>

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biomformat.pdf |biomformat.html✨
biomformat/json (API)
NEWS

# Install 'biomformat' in R:
install.packages('biomformat', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/joey711/biomformat/issues

On BioConductor:biomformat-1.33.0(bioc 3.20)biomformat-1.32.0(bioc 3.19)

immunooncologydataimportmetagenomicsmicrobiome

10.33 score 7 stars 39 packages 374 scripts 8.7k downloads 16 exports 8 dependencies

Last updated 25 days agofrom:a3d34c3bff. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:biombiom_databiom_shapecolnamesheadermake_biommatrix_element_typencolnrowobservation_metadataread_biomread_hdf5_biomrownamessample_metadatashowwrite_biom

Dependencies:jsonlitelatticeMatrixplyrRcpprhdf5rhdf5filtersRhdf5lib

The biomformat package vignette

Paul J. McMurdie

Rendered frombiomformat.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2016-04-16
Started: 2015-12-01

Readme and manuals

Help Manual

Help pageTopics
This is an R package for interfacing with the biom format.biom-package
Build and return an instance of the biom-class.biom biom,list-method
Access main data observation matrix data from 'biom-class'.biom_data biom_data,biom,ANY,character-method biom_data,biom,character,ANY-method biom_data,biom,missing,missing-method biom_data,biom,missing,numeric-method biom_data,biom,numeric,missing-method biom_data,biom,numeric,numeric-method
The matrix dimensions of a 'biom-class' object.biom_shape biom_shape,biom-method
The biom format data class.biom-class
Method extensions to 'colnames' for 'biom-class' objects.colnames,biom-method
Extract the header from a 'biom-class' object as a list.header header,biom-method
Create a 'biom-class' from 'matrix-class' or 'data.frame'.make_biom
Access class of data in the matrix elements of a 'biom-class' objectmatrix_element_type matrix_element_type,biom-method
Method extensions to 'ncol' for 'biom-class' objects.ncol,biom-method
Method extensions to 'nrow' for 'biom-class' objects.nrow,biom-method
Access observation (row) meta data from 'biom-class'.observation_metadata observation_metadata,biom,character-method observation_metadata,biom,missing-method observation_metadata,biom,numeric-method
Read a biom-format file, returning a 'biom-class'.read_biom
Read in a biom-format vs 2 file, returning a 'list'.read_hdf5_biom
Method extensions to 'rownames' for 'biom-class' objects.rownames,biom-method
Access meta data from 'biom-class'.sample_metadata sample_metadata,biom,character-method sample_metadata,biom,missing-method sample_metadata,biom,numeric-method
Method extensions to show for biom objects.show,biom-method
Write a biom-format v1 file, returning a 'biom-class'.write_biom