Installation

It is advised not to have any packages loaded when installing DAtest. Installation of DAtest and all dependencies has been tested to work on a clean R version 3.5.1 by installing in the following order:

The DAtest package:

if (!requireNamespace("devtools")) install.packages("devtools")

# Developmental version (this tutorial is written for this version, recommended):
devtools::install_github("Russel88/DAtest")

# Version associated with bioRxiv paper:
# devtools::install_github("Russel88/[email protected]")

Main difference between bioRxiv version and developmental version is that the developmental version includes a "Score" that can be used to rank the different methods. This Score is a combination of False Discovery Rate (FDR), spike detect rate (empirical power) and Area under the ROC Curve (AUC). The general approach is still the same as described in the paper. The developmental version also includes additional methods and several bug fixes. See details on the changes here.

The following packages are needed for full functionality

if (!requireNamespace("BiocManager")) install.packages("BiocManager")

BiocManager::install(c("DESeq2","limma","edgeR","metagenomeSeq","baySeq","ALDEx2","qvalue","impute"))

install.packages(c("samr","pscl","statmod","mvabund"))) 

# RAIDA has to be installed from external sources:
## Dependencies (after the bioconductor packages are installed)
install.packages(c("shiny","exactRankTests","openxlsx","protoclust","DT","coin","stringr"))

## RAIDA:
install.packages("https://cals.arizona.edu/~anling/software/RAIDA_1.0.tar.gz",repos = NULL)

Note: If installation fails for any of these additional packages, do not despair. DAtest will work seamlessly, but will simply exclude methods that depends on these packages.

The following are suggested, but not needed:

# For drawing Venn diagrams
install.packages("eulerr")

# For post-hoc testing (generalized) linear models
install.packages("lsmeans")

# Phyloseq, for organizing microbiome data
BiocManager::install("phyloseq")