Downloading XHMM

The XHMM program and source code is currently available to download under the GPL (GNU General Public License) v3.

Git repository

The XHMM Git repository contains the core C++ code in addition to various useful scripts. Specifically, the always up-to-date "development" zip file is found here.

The scripts include tools for:

Visualization of the PCA and the called CNVs
Conversion of XHMM's .xcnv format to PLINK's .cnv format

Installing XHMM

XHMM was developed assuming compilation on Linux with gcc version 4.4. Other requirements are the pthread and lapack C libraries.

[Also, to modify the command-line options, it is necessary to install Gengetopt (recommended version 2.22 or higher).]

Uncompress the xhmm zip file, where you want to install it:
unzip master.zip

Change to the xhmm directory:
cd statgen-xhmm-*

Run make to install the software (which starts by automatically compiling the included hmm++ library):
make

Installing / using the XHMM R scripts

The XHMM R code is now available as an R library. There are still two options for using the scripts:

Newer (preferred) option

Install the xhmmScripts package via one of the following methods (you only need to do this once):

Compile it from the main XHMM source code downloaded from the Git repository above:
cd statgen-xhmm-* make R
Then, run in R:
install.packages(list.files(path=".", pattern="xhmmScripts_.+\\.tar\\.gz"), repos=NULL, type="source")

Download and install the package from CRAN using the install.packages() command in R:
install.packages("xhmmScripts")

Download it from the xhmmScripts page at CRAN. Then, run in R:
install.packages(list.files(path=".", pattern="xhmmScripts_.+\\.tar\\.gz"), repos=NULL, type="source")

To use the R code, preface your R scripts with:
```
library(xhmmScripts)
```

Older option

Directly source the R code found in the downloaded source code, by running the following at the top of your R scripts:

XHMM_PATH = "./"
XHMM_SCRIPTS_PATH = paste(XHMM_PATH, "/sources/scripts/R_functions", sep="")
source(paste(XHMM_SCRIPTS_PATH, "/sourceDir.R", sep=""))
sourceDir(XHMM_SCRIPTS_PATH, trace = FALSE, recursive = TRUE)

library(gplots)
library(plotrix)