Convert phyloseq OTU count data into DGEList for edgeR package

Usage

phyloseq_to_edgeR(physeq, group, method = "RLE", ...)

Arguments

physeq

(required): a phyloseq-class object obtained using the phyloseq package.

group

(required) A character vector or factor giving the experimental group/condition for each sample/library. Alternatively, you may provide the name of a sample variable. This name should be among the output of sample_variables(physeq), in which case get_variable(physeq, group) would return either a character vector or factor. This is passed on to DGEList, and you may find further details or examples in its documentation.

method

The label of the edgeR-implemented normalization to use. See calcNormFactors for supported options and details. The default option is "RLE", which is a scaling factor method proposed by Anders and Huber (2010). At time of writing, the edgeR package supported the following options to the method argument:

c("TMM", "RLE", "upperquartile", "none").

...

Additional arguments passed on to DGEList

Value

A DGEList object. See edgeR::estimateTagwiseDisp() for more details.