phyloseq2DESeq2: Convert 'phyloseq-class' object to 'DESeqDataSet-class'...

In yiluheihei/microbiomeMarker: microbiome biomarker analysis toolkit

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)

yiluheihei/microbiomeMarker documentation built on Nov. 5, 2023, 7:19 a.m.