OATHX

Open GWAS algoriTHm (OATH) for naive summary statistics.

It uses naive summary statistics, which are generated by nss, into their various models.

---

Master command: oathX

Option

--nss-batch

Specify the nss-batch file. It is the *.list.nss file generated in gear nss.

--cm

Specify the correlation file. It is the *.m.nss file generated in gear nss.

--keep-batch

Specify the index of the files listed in nss-batch. If it is not specified, all files listed in --nss-batch will be used for oath analysis.

--n

Specify the sample size.

--verbose

All regression parameters will be printed out.

--out

Specify the root for the output file.

Examples

java -jar gear.jar nss --bfile test --pheno test.phe --mpheno 1 --covar test.cov --covar-number 1 2 4 --out test
java -jar gear.jar oathX --nss-batch test.list.nss --cm test.m.nss --n 200 --out test

Notes: test.list.nss and test.m.nss are both generated by nss.

For this example, test.list.nss will include

test.p.1.nss #naive summary statistics for phenotype
test.c.1.nss #naive summary statistics for covariate 1
test.c.2.nss #naive summary statistics for covariate 3
test.c.4.nss #naive summary statistics for covariate 4

--n, the sample size is the number of samples used in nss.

If only a specific model is interested, then oath subcommand can be used

java -jar gear.jar oath --nss-batch test.list.nss --cm test.m.nss --n 200 --keep-nss 1 3 --out test

"--keep 1 3" indicates test.p.1.nss and test.c.2.nss will be used for analysis.