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]