run_DAF_analysis: Run differentially abundant features analysis.

In LeoStafu/metaDAF: Metagenomics tools for detecting Differentially Abundant Features

Description

Call a specific processing function depending on the method chosen. Input data are generated by the build_DAF_data function.

Usage

run_DAF_analysis(data, method = c("deseq2", "mbzinb", "zibseq", "raida",
  "aldex2", "metagenomeseq", "edger", "voom", "wilcox"), verbose = FALSE,
  ...)

Arguments

data	a list. the returned object of the build_DAF_data function
method	The name of the method to use for DAF detection. Any unambiguous abbreviation of "deseq2", "mbzinb", "zibseq", "raida", "aldex2", "metagenomeseq", "edger", "voom" or "wilcox". Default is "deseq2".
verbose	logical. Should processing function display all of their messages
...	additional parameters to be passed to the processing function.

Details

The function will first assess if the input data is a single dataset or a list of several of them. Then it will check is one or more methods are called. Based on these information, several kind of analysis are performed : a simple one, a repeated one (focus on one method and average results), a compared one (multiple methods called one time) or a compared and repeated one (several methods, several times).

Value

Data frame containing the pvalue and the adjusted pvalue (BH) of the differential analysis as well as the names of methods and number of runs.

LeoStafu/metaDAF documentation built on July 14, 2019, 6:41 p.m.