README.md

In fairmiracle/AMOUNTAIN: Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach

Bioconductor page http://bioconductor.org/packages/AMOUNTAIN

Installation

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")

Compile on Linux

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 |

Compile on Windows

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.

Refererence

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

fairmiracle/AMOUNTAIN documentation built on May 16, 2019, 9:59 a.m.