This is the accompanying R package for the DEEPN project.
deepn has several package dependencies, most notably JAGS and Bioconductor. JAGS must be setup outside R (see link for instructions), while Bioconductor can be installed within R via:
source("https://bioconductor.org/biocLite.R")
biocLite()Once that is done, you can install deepn via devtools (which itself can be installed via install.packages("devtools")):
devtools::install_github("pbreheny/deepn")Once installed, deepn can be used to analyze the output from deepn with
require(deepn)
analyzeDeepn("deepn.config")where "deepn.config" is the name of the configuration file that DEEPN outputs containing path names to all the .csv files needed in the analysis. This will create a file, stat.csv, containing a table of summary statistics for each gene.
The above analysis may take a while to run, depending on the threshold. To run a "quick" version of the analysis, you can use
analyzeDeepn("deepn.config", debug=TRUE)which applies a very high PPM threshold of 200 prior to analysis, so that it should only take a minute or two to complete.