PROGRAM: GWGGI
DESCRIPTION: Genome Wide Joint Association Software
AUTHOR: Changshuai Wei
CONTACT: [email protected]
YEAR: 2011
Precompiled excutable for windows and unix, as well as example data can be found at http://changshuaiwei.github.io/software.html#GWGGI
COMPILATION: You will need a standard C/C++ compiler such as GNU gcc (version 3).
Using TAMW:
gwggi --bfile example --tamw --converge --ntree 2000 --clsf-sqrt --tree-depth 4 --showntree --out ex.rst
Using LRMW:
gwggi --bfile example --lmw --showcv --maxauc 0.99 --out ex.rst
##Data format
GWGGI can read plink binary format, using --bfile filename.
GWGGI can also read text format, using --file filename.
##Likelihood Ratio Forword Mann-Whitney
Fast forward searching higher order joint association, using --lmw.
Example: gwggi --bfile filename --lmw --out resultfile.
More complicated example: gwggi --bfile filename --lmw --hz --hiorder 10 --maxauc 0.99 --out resultfile
##Trees Assembling Mann-Whitney
Assembling multiple trees to search low-marginal effect, using --tamw.
Example: gwggi --bfile filename --tamw --out resultfile.
More complicated example: gwggi --bfile filename --tamw --converge --ntree 10000 --td-burnin --showntree --out resultfile
##Options&Functions ###Functions
--bfile string, read binary file
--file string, read text file
--out string, file for output
--lmw, Likelihood Ratio Mann-Whitney
--lmw-apl string, apply lmw to a new data
--tamw, Trees Assembling Mann-Whitney
--tamw-apl, apply tamw to a new data
###Options
--hz, allow heterozygosity ( Aa v.s. aa,AA )
--hiorder int, define the highest order for searching, default is 10
--maxauc float, define the highest auc for searching, default is 0.9
--converge, show the converging status of tamw in *.monitor file
--ntree int, number of trees in tamw, default is 2000
--tree-depth int, set tree depth, default is 6
--td-burnin, use first 50 bootstrap sample to determine the trees depth
--showntree, show the number of tree built as program is running
--clsf int, number of genetic variants randomly selected in tamw
--clsf-sqrt, using sqrt of total genetic variant for --clsf in tamw, default is ln
--showcv, show the progress of the program when runing lmw
--no-cv, scaning without cross-validation for lmw
--lr-sub string, output the subject specific LR value