sample_data<- {phyloseq} | R Documentation

## Assign (new) sample_data to `x`

### Description

This replaces the current `sample_data` component of `x` with `value`, if `value` is a `sample_data-class`. However, if `value` is a `data.frame`, then `value` is first coerced to a `sample_data-class`, and then assigned. Alternatively, if `value` is `phyloseq-class`, then the `sample_data` component will first be accessed from `value` and then assigned. This makes possible some concise assignment/replacement statements when adjusting, modifying, or building subsets of experiment-level data. See some examples below.

Internally, this re-builds the `phyloseq-class` object using the standard `phyloseq` constructor. Thus, index mismatches between sample-describing components will not be allowed, and subsetting will occurr automatically such that only the intersection of sample IDs are included in any components. This has the added benefit of re-checking (internally) for any other issues.

### Usage

    sample_data(x) <- value

### Arguments

`x` | (Required). `phyloseq-class`. The object to modify.
`value` | (Required). Either a `sample_data-class`, a `data.frame` that can be coerced into `sample_data-class`, or a `phyloseq-class` that contains a suitable `sample_data` component to assign to `x`. If unsure, try `sample_data``(value)`, which should return a `sample_data-class` object without error.

### Value

No return. This is an assignment statement.

### Examples

     data(soilrep)
     soilrep
     head(sample_data(soilrep))
     sample_data(soilrep)$Time <- as.integer(substr(sample_data(soilrep)$Sample, 1, 1))
     head(sample_data(soilrep))

[Package phyloseq version 1.28.0 Index]