subset: Subset an rbiom object by sample names or metadata.

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

Subset an rbiom object by sample names or metadata.

Description

Subset an rbiom object by sample names or metadata.

Usage

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

## S3 method for class 'rbiom'
biom[i]

Arguments

biom	An rbiom object, such as from as_rbiom().
...	Passed on to 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

Value

An rbiom object.

See Also

Other transformations: mutate(), rarefy(), rarefy_cols(), slice()

Examples

    library(rbiom) 
    
    # Subset to specific samples
    biom <- hmp50[c('HMP20', 'HMP42', 'HMP12')]
    biom$metadata
    
    # Subset according to metadata (using base::subset)
    biom <- subset(hmp50, `Body Site` %in% c('Saliva') & Age < 25)
    biom$metadata

cmmr/rbiom documentation built on Feb. 16, 2024, 3:34 a.m.