phyloseq_to_deseq2 {phyloseq} | R Documentation

## Convert phyloseq data to DESeq2 dds object

### Description

No testing is performed by this function. The phyloseq data is converted to the relevant `DESeqDataSet` object, which can then be tested in the negative binomial generalized linear model framework of the `DESeq` function in DESeq2 package. See the phyloseq-extensions tutorials for more details.

### Usage

    phyloseq_to_deseq2(physeq, design, ...)

### Arguments

`physeq` | (Required). `phyloseq-class`. Must have a `sample_data` component.
`design` | (Required). A `formula` which specifies the design of the experiment, taking the form `formula(~ x + y + z)`. That is, a formula with right-hand side only. By default, the functions in this package and DESeq2 will use the last variable in the formula (e.g. `z`) for presenting results (fold changes, etc.) and plotting. When considering your specification of experimental design, you will want to re-order the levels so that the `NULL` set is first. For example, the following line of code would ensure that Enterotype 1 is used as the reference sample class in tests by setting it to the first of the factor levels using the `relevel` function: `sample_data(entill)$Enterotype <- relevel(sample_data(entill)$Enterotype, "1")`
`...` | (Optional). Additional named arguments passed to `DESeqDataSetFromMatrix`. Most users will not need to pass any additional arguments here. Most testing-related options should be provided in a following call to `DESeq`.

### Value

A `DESeqDataSet` object.

### See Also

`vignette("phyloseq-mixture-models")`

The phyloseq-extensions tutorials.

`DESeq`

`results`

`DESeqDataSetFromMatrix`

### Examples

     # Check out the vignette phyloseq-mixture-models for more details.
     # vignette("phyloseq-mixture-models")
     data(soilrep)
     phyloseq_to_deseq2(soilrep, ~warmed)

[Package phyloseq version 1.38.0 Index]