More Usage Examples¶
For checking all the optional arguments, please use –help.
$ GenEpi --help
You will obtain the following argument list:
usage: GenEpi [-h] -g G -p P [-s S] [-o O] [-m {c,r}] [-k K] [-t T]
[--updatedb] [-b {hg19,hg38}] [--compressld] [-d D] [-r R]
optional arguments:
-h, --help show this help message and exit
-g G filename of the input .gen file
-p P filename of the input phenotype
-s S self-defined genome regions
-o O output file path
-m {c,r} choose model type: c for classification; r for regression
-k K k of k-fold cross validation
-t T number of threads
update UCSC database:
--updatedb enable this function
-b {hg19,hg38} human genome build
compress data by LD block:
--compressld enable this function
-d D threshold for compression: D prime
-r R threshold for compression: R square
Applying on Your Data¶
$ GenEpi -g full_path_of_your_.GEN_file -p full_path_of_your_.CSV_file -o ./
For Quantitative Study¶
GenEpi can support both case/control and quantitative studies, for quantitative studies please modify the parameter -m. You could download the test data and excute the following command.
$ GenEpi -g sample.gen -p sample_q.csv -o ./ -m r
Changing the Genome Build¶
For changing the build of USCS genome browser, please modify the parameter -b.
$ GenEpi -g example -p example -o ./ --updatedb -b hg38
Threshold for Dimension Reduction¶
You could modify the threshold for Linkage Disequilibrium dimension reduction by following command.
$ GenEpi -g example -p example -o ./ --compressld -d 0.9 -r 0.9