limix.qtl.QTLModel

class limix.qtl.QTLModel(null_lml, alt_lmls, effsizes, null_covariate_effsizes)

Result of a QTL analysis.

An instance of this class is returned by limix.qtl.scan().

__init__(null_lml, alt_lmls, effsizes, null_covariate_effsizes)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(null_lml, alt_lmls, effsizes, …)

Initialize self.

Attributes

alt_lmls	Log of the marginal likelihoods across tested variants.
null_covariate_effsizes	Covariate effect-sizes under the null hypothesis.
null_lml	Log of the marginal likelihood under the null hypothesis.
variant_effsizes	Variant effect-sizes.
variant_effsizes_se	Standard errors of the variant effect sizes.
variant_pvalues	Variant p-values.

alt_lmls

Log of the marginal likelihoods across tested variants.

Returns:Log of marginal likelihoods. Return type:array_like

null_covariate_effsizes

Covariate effect-sizes under the null hypothesis.

Returns:Estimated covariant effect sizes under the null hypothesis. Return type:array_like

null_lml

Log of the marginal likelihood under the null hypothesis.

Returns:Log of marginal likelihood. Return type:float

variant_effsizes

Variant effect-sizes.

Returns:Estimated variant effect sizes. Return type:array_like

variant_effsizes_se

Standard errors of the variant effect sizes.

Returns:Estimated standard errors of the variant effect sizes. Return type:array_like

variant_pvalues

Variant p-values.

Returns:Association significance between variant and phenotype. Return type:array_like