OATH bus

Reproducibility and deep evaluation using OATH

For a GWAS model, it often reports one of the possible results given a set of covariates. For example, for a saturated model y=a+bx+b1*c1+b2*c2+b3*c3+3, in which x is the target marker and c* are nuisance parameters, it is possible to have 8 estimates for b:

1) y=a+bx+e
2) y=a+bx+b1*c1+e
3) y=a+bx+b2*c2+e
4) y=a+bx+b3*c3+e
5) y=a+bx+b1*c1+b2*c2+e
6) y=a+bx+b1*c1+b3*c3+e
7) y=a+bx+b2*c2+b3*c3+e
8) y=a+bx+b1*c1+b2*c2+b3*c3+e

This function will automatically generate all these eight models for a chosen set of covariates.

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Master command: oath-bus

Options

--bfile

Specify the genotype files in binary format.

--pheno

Specify the phenotype file.

--mpheno

Specify the index for the phenotype file. It is defaulted to 1.

--covar

Specify the covariate file. Note, here the covariate file is directly used to generate nss rather than as adjustment for the phenotype.

--covar-number

Specify the indexes for the covariates.

--maf

specify the maf cutoff. It is defaulted to 0.05.

--keep

Specify the samples for analysis.

Example

java -jar gear.jar oath-bus --bfile test --pheno test.phe --mpheno 1 --covar test.cov --covar-number 1 2 3 --out test

It will generate models

1) y=a+bx+e
2) y=a+bx+b1*c1+e
3) y=a+bx+b2*c2+e
4) y=a+bx+b3*c3+e
5) y=a+bx+b1*c1+b2*c2+e
6) y=a+bx+b1*c1+b3*c3+e
7) y=a+bx+b2*c2+b3*c3+e
8) y=a+bx+b1*c1+b2*c2+b3*c3+e