subset: Subset an rbiom object by sample names, OTU names, metadata,...

In rbiom: Read/Write, Analyze, and Visualize 'BIOM' Data

Subset an rbiom object by sample names, OTU names, metadata, or taxonomy.

Description

Dropping samples or OTUs will lead to observations being removed from the OTU matrix (biom$counts). OTUs and samples with zero observations are automatically removed from the rbiom object.

Usage

## S3 method for class 'rbiom'
subset(x, subset, clone = TRUE, ...)

## S3 method for class 'rbiom'
x[i, j, ..., clone = TRUE, drop = FALSE]

## S3 method for class 'rbiom'
na.omit(object, fields = ".all", clone = TRUE, ...)

subset_taxa(x, subset, clone = TRUE, ...)

Arguments

x	An rbiom object, such as from as_rbiom().
subset	Logical expression for rows to keep. See base::subset().
clone	Create a copy of biom before modifying. If FALSE, biom is modified in place as a side-effect. See speed ups for use cases. Default: TRUE
...	Not used.
i, j	The sample or OTU names to keep. Or a logical/integer vector indicating which sample names from biom$samples or biom$otus to keep. Subsetting with ⁠[i]⁠ takes i as samples, whereas ⁠[i,j]⁠ takes i as otus and j as samples (corresponding to ⁠[rows, cols]⁠ in the underlying biom$counts matrix).
drop	Not used
object	An rbiom object, such as from as_rbiom().
fields	Which metadata field(s) to check for NAs, or ".all" to check all metadata fields.

Value

An rbiom object.

See Also

Other transformations: modify_metadata, rarefy(), rarefy_cols(), slice_metadata, with()

Examples

    library(rbiom)
    library(dplyr)
    
    # Subset to specific samples
    biom <- hmp50[c('HMP20', 'HMP42', 'HMP12')]
    biom$metadata
    
    # Subset to specific OTUs
    biom <- hmp50[c('LtbAci52', 'UncO2012'),] # <- Trailing ,
    biom$taxonomy
    
    # Subset to specific samples and OTUs
    biom <- hmp50[c('LtbAci52', 'UncO2012'), c('HMP20', 'HMP42', 'HMP12')]
    as.matrix(biom)
    
    # Subset samples according to metadata
    biom <- subset(hmp50, `Body Site` %in% c('Saliva') & Age < 25)
    biom$metadata
    
    # Subset OTUs according to taxonomy
    biom <- subset_taxa(hmp50, Phylum == 'Cyanobacteria')
    biom$taxonomy
    
    # Remove samples with NA metadata values
    biom <- mutate(hmp50, BS2 = na_if(`Body Site`, 'Saliva'))
    biom$metadata
    biom <- na.omit(biom)
    biom$metadata

rbiom documentation built on April 3, 2025, 6:39 p.m.