Version: 1.2.5
HIBAG is a state of the art software package for imputing HLA types using SNP data, and it uses the R statistical programming language. HIBAG can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and HLA types. Attribute bagging is a technique which improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection.
GNU General Public License, GPLv3
Xiuwen Zheng (zhengxwen@gmail.com / zhengx@u.washington.edu)
Zheng, X. et al. HIBAG-HLA genotype imputation with attribute bagging. The pharmacogenomics journal 14, 192–200 (2014). http://dx.doi.org/10.1038/tpj.2013.18
Wiki Page: https://github.com/zhengxwen/HIBAG/wiki
library("devtools")
install_github("zhengxwen/HIBAG")
The install_github()
approach requires that you build from source, i.e. make
and compilers must be installed on your system -- see the R FAQ for your operating system; you may also need to install dependencies manually.
HIBAG
r-forge repository:install.packages("HIBAG", repos="http://R-Forge.R-project.org")
wget --no-check-certificate https://github.com/zhengxwen/HIBAG/tarball/master -O HIBAG_latest.tar.gz
** Or **
curl -L https://github.com/zhengxwen/HIBAG/tarball/master/ -o HIBAG_latest.tar.gz
** Install **
R CMD INSTALL HIBAG_latest.tar.gz
Change "~/.R/Makevars" to, if your machine supports SSE4.2 or higher AVX:
## for C code
CFLAGS=-g -O3 -march=native
## for C++ code
CXXFLAGS=-g -O3 -march=native
Or force to create hardware POPCNT code:
## for C code
CFLAGS=-g -O3 -msse4.2 -mpopcnt
## for C++ code
CXXFLAGS=-g -O3 -msse4.2 -mpopcnt
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.