rbiom_objects: Working with rbiom Objects.
In cmmr/rbiom: Read/Write, Analyze, and Visualize 'BIOM' Data
rbiom_objects R Documentation
Working with rbiom Objects.
Description
Rbiom objects make it easy to access and manipulate your BIOM data, ensuring
all the disparate components remain in sync. These objects behave largely
like lists, in that you can access and assign to them using the $
operator. The sections below list all the fields which can be read and/or
written, and the helper functions for common tasks like rarefying and
subsetting. To create an rbiom object, see as_rbiom().
Use $clone() to create a copy of an rbiom object. This is necessary
because rbiom objects are passed by reference. The usual <- assignment
operator will simply create a second reference to the same object - it will
not create a second object. See speed ups for more details.
Readable Fields
Reading from fields will not change the rbiom object.
Accessor Content
$counts Abundance of each OTU in each sample.
$metadata Sample mappings to metadata (treatment, patient, etc).
$taxonomy OTU mappings to taxonomic ranks (genus, phylum, etc).
$otus, $n_otus OTU names.
$samples, $n_samples Sample names.
$fields, $n_fields Metadata field names.
$ranks, $n_ranks Taxonomic rank names.
$tree, $sequences Phylogenetic tree / sequences for the OTUs, or NULL.
$id, $comment Arbitrary strings for describing the dataset, or NULL.
$depth Rarefaction depth, or NULL if unrarefied.
$date Date from BIOM file.
Writable Fields
Assigning new values to these components will trigger
validation checks and inter-component synchronization.
Component What can be assigned.
$counts matrix of abundances; OTUs (rows) by samples (columns)
$metadata data.frame with '.sample' column, or a file name
$taxonomy data.frame with '.otu' as the first column
$otus character vector with new names for the OTUs
$samples character vector with new names for the samples
$tree phylo object with the phylogenetic tree for the OTUs
$sequences character vector of OTU reference sequences
$id, $comment string with a title or comment for the dataset
$date date-like object, or "%Y-%m-%dT%H:%M:%SZ" string
Transformations
All functions return an rbiom object.
Function Transformation
<rbiom>$clone() Safely duplicate an rbiom object.
cmmr/rbiom documentation built on April 28, 2024, 6:38 a.m.
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| rbiom_objects | R Documentation |
Working with rbiom Objects.
Description
Rbiom objects make it easy to access and manipulate your BIOM data, ensuring
all the disparate components remain in sync. These objects behave largely
like lists, in that you can access and assign to them using the $
operator. The sections below list all the fields which can be read and/or
written, and the helper functions for common tasks like rarefying and
subsetting. To create an rbiom object, see as_rbiom().
Use $clone() to create a copy of an rbiom object. This is necessary
because rbiom objects are passed by reference. The usual <- assignment
operator will simply create a second reference to the same object - it will
not create a second object. See speed ups for more details.
Readable Fields
Reading from fields will not change the rbiom object.
| Accessor | Content |
$counts | Abundance of each OTU in each sample. |
$metadata | Sample mappings to metadata (treatment, patient, etc). |
$taxonomy | OTU mappings to taxonomic ranks (genus, phylum, etc). |
$otus, $n_otus | OTU names. |
$samples, $n_samples | Sample names. |
$fields, $n_fields | Metadata field names. |
$ranks, $n_ranks | Taxonomic rank names. |
$tree, $sequences | Phylogenetic tree / sequences for the OTUs, or NULL. |
$id, $comment | Arbitrary strings for describing the dataset, or NULL. |
$depth | Rarefaction depth, or NULL if unrarefied. |
$date | Date from BIOM file. |
Writable Fields
Assigning new values to these components will trigger validation checks and inter-component synchronization.
| Component | What can be assigned. |
$counts | matrix of abundances; OTUs (rows) by samples (columns) |
$metadata | data.frame with '.sample' column, or a file name |
$taxonomy | data.frame with '.otu' as the first column |
$otus | character vector with new names for the OTUs |
$samples | character vector with new names for the samples |
$tree | phylo object with the phylogenetic tree for the OTUs |
$sequences | character vector of OTU reference sequences |
$id, $comment | string with a title or comment for the dataset |
$date | date-like object, or "%Y-%m-%dT%H:%M:%SZ" string |
Transformations
All functions return an rbiom object.
| Function | Transformation |
<rbiom>$clone() | Safely duplicate an rbiom object. |
|
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