Bioconductor page http://bioconductor.org/packages/AMOUNTAIN
Install the stable version from Bioconductor
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("AMOUNTAIN")
Install the development version from Github
library(devtools)
install_github("fairmiracle/AMOUNTAIN")
Make sure GSL in installed, type gsl-config in terminal.
To compile C code:
git clone https://github.com/fairmiracle/AMOUNTAIN.git
cd AMOUNTAIN
gcc -c src/AMOUNTAIN.c -fPIC -std=c99
gcc -shared -o src/AMOUNTAIN.so AMOUNTAIN.o -lgsl -lgslcblas
rm AMOUNTAIN.o
To use C version functions in R:
source('R/AMOUNTAIN.R')
dyn.load(paste("src/AMOUNTAIN", .Platform$dynlib.ext, sep = ""))
source('R/AMOUNTAINC.R')
Here is a table of C-version functions and pure R functions:
| C-version | Pure R | Brief description |
|---|---|---|
CGPFixSS |
moduleIdentificationGPFixSS |
Module identification on single network |
CGPFixSSTwolayer |
moduleIdentificationGPFixSSTwolayer |
Module identification on two-layer network |
CGPFixSSMultiLayer |
moduleIdentificationGPFixSSMultilayer |
Module identification on multi-layer network |
It is not that straightforward to compile with GSL under Windows. Someone has created GSL Windows DLL and headers for both 32 and 64-bit in https://code.google.com/archive/p/oscats/downloads. Extract gsl-1.15-dev-win32.zip and gsl-1.15-dev-win64.zip into two directories:
- C:\GSL\i386
- C:\GSL\x64
and set the environment variable LIB_GSL as C:/GSL instead of C:\GSL. Finally add C:\GSL\x64\bin to the Path in case missing the DLLs. Then the source can be compiled.
Dong Li, Shan He, Zhisong Pan, Guyu Hu. Active modules for multilayer weighted gene co-expression networks: a convex optimization approach. biorxiv 2016. http://www.biorxiv.org/content/early/2016/06/03/056952