NSS

Generating naive summary statistics for GWAS data.

It generates naive summary statistics (nss) for a saturated model. For example, for the saturated model y=a+b0x+b1*c1+b2*c2+e, in which x is the target marker and c* are nuisance parameters. This function generates naive summary statistics for the following naive linear regressions,

y=a+b0*x+e
y=a+b1*c1+e
y=a+b2*c2+e
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and save these naive summary statistics into respective files.

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**Master command:** nss

**Options**

--bfile <arg>

Specify the genotype files in binary format.

--pheno <arg>

Specify the phenotype file.

--mpheno <arg>

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

--covar <arg>

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

--covar-number <args>

Specify the indexes for the covariates.

--maf <arg>

specify the maf cutoff. It is defaulted to 0.05.

--keep <arg>

Specify the samples for analysis.

Examples

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

Output files

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test.p.1.nss is for nss generated for the phenotype selected.
test.c.X.nss is for nss generated for the xth covariate.
test.m.nss is the correlation matrix for phenotype and covariates.
test.list.nss is a list for the nss files generated.
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All these output files can be load to [OATH] (https://github.com/gc5k/GEAR/wiki/OATH).