phyloseq2DESeq2 {microbiomeMarker}R Documentation

Convert phyloseq-class object to DESeqDataSet-class object

Description

This function convert [phyloseq::phyloseq-class] to [DESeq2::DESeqDataSet-class], which can then be tested using [DESeq2::DESeq()'].

Usage

phyloseq2DESeq2(ps, design, ...)

Arguments

ps

the [phyloseq::phyloseq-class] object to convert, which must have a [phyloseq::sample_data()'] component.

design

a formula or matrix, the formula expresses how the counts for each gene depend on the variables in colData. Many R formula are valid, including designs with multiple variables, e.g., ~ group + condition. This argument is passed to DESeq2::DESeqDataSetFromMatrix().

...

additional arguments passed to DESeq2::DESeqDataSetFromMatrix(), Most users will not need to pass any additional arguments here.

Value

a DESeq2::DESeqDataSet object.

See Also

DESeq2::DESeqDataSetFromMatrix(),DESeq2::DESeq()

Examples

data(caporaso)
phyloseq2DESeq2(caporaso, ~SampleType)

[Package microbiomeMarker version 1.0.0 Index]