spy_to_limma: Linear model using limma on different phylogenic levels

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

Description

Fit linear models using the limma package to a SummarizedPhyloseq object. See the lmFit for more detail.

Usage

spy_to_limma(spy, design, transform = function(x) {     log2(x + 1) },
  coef, p.value, ...)

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
transform	(required) The method to use to transform the data before fitting linear model. "log" will apply a log transform to the data while "none" won't do anything.
coef	(required) The index number or name of the coefficient (variable) for building the results tables. The value provided must be one of the colnames or indices of the design matrix. This argument is corresponding to the coef in the topTable from the limma package.
p.value	(required) Same as coef
...	(optional) Other parameters to be parsed to the topTable function

Note

the limma 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.