spy_to_deseq2: Conduct DESeq2 analysis on different phylogenic levels

In zhuchcn/phylox: Analyzing and Visualization Microbiome Data on Different Phylogenic Levels

Description

Conduct differential expression using the DESeq2 package to a SummarizedPhyloseq object. See the DESeq for more detail.

Usage

spy_to_deseq2(spy, design, resultsName, ...)

Arguments

spy	(required) SummarizedPhyloseq-class
design	(required) The design matrix of the experiment, with rows corresponding to sample IDs and columns to coefficients to be estimated. This can be constructed using model.matrix function
resultsName	The index or name of the coefficient (variable) for building the results tables. The value provided must be one of the colnames of the design matrix. This argument is corresponding to the name in the results from the DESeq2 package.
...	(optional) Other parameters to be parsed to the DESeq function

Note

The DESeq2 package needs to be installed in order to successfully run this function.

Author(s)

Chenghao Zhu

zhuchcn/phylox documentation built on May 31, 2019, 5:14 p.m.