trtools.associaTR module

class trtools.associaTR.OLS(endog, exog=None, missing='none', hasconst=None, **kwargs)

Bases: statsmodels.regression.linear_model.WLS

A simple ordinary least squares model.

Parameters

  • endog (array-like) – 1-d endogenous response variable. The dependent variable.

  • exog (array-like) – A nobs x k array where nobs is the number of observations and k is the number of regressors. An intercept is not included by default and should be added by the user. See statsmodels.tools.add_constant().

  • missing (str) – Available options are ‘none’, ‘drop’, and ‘raise’. If ‘none’, no nan checking is done. If ‘drop’, any observations with nans are dropped. If ‘raise’, an error is raised. Default is ‘none.’

  • hasconst (None or bool) – Indicates whether the RHS includes a user-supplied constant. If True, a constant is not checked for and k_constant is set to 1 and all result statistics are calculated as if a constant is present. If False, a constant is not checked for and k_constant is set to 0.

weights

Has an attribute weights = array(1.0) due to inheritance from WLS.

Type

scalar

See also

GLS

Examples

>>> import numpy as np
>>>
>>> import statsmodels.api as sm
>>>
>>> Y = [1,3,4,5,2,3,4]
>>> X = range(1,8)
>>> X = sm.add_constant(X)
>>>
>>> model = sm.OLS(Y,X)
>>> results = model.fit()
>>> results.params
array([ 2.14285714,  0.25      ])
>>> results.tvalues
array([ 1.87867287,  0.98019606])
>>> print(results.t_test([1, 0]))
<T test: effect=array([ 2.14285714]), sd=array([[ 1.14062282]]), t=array([[ 1.87867287]]), p=array([[ 0.05953974]]), df_denom=5>
>>> print(results.f_test(np.identity(2)))
<F test: F=array([[ 19.46078431]]), p=[[ 0.00437251]], df_denom=5, df_num=2>

Notes

No constant is added by the model unless you are using formulas.

_fit_ridge(alpha)

Fit a linear model using ridge regression.

Parameters

alpha (scalar or array-like) – The penalty weight. If a scalar, the same penalty weight applies to all variables in the model. If a vector, it must have the same length as params, and contains a penalty weight for each coefficient.

Notes

Equivalent to fit_regularized with L1_wt = 0 (but implemented more efficiently).

fit_regularized(method='elastic_net', alpha=0.0, L1_wt=1.0, start_params=None, profile_scale=False, refit=False, **kwargs)

Return a regularized fit to a linear regression model.

Parameters

  • method (string) – ‘elastic_net’ and ‘sqrt_lasso’ are currently implemented.

  • alpha (scalar or array-like) – The penalty weight. If a scalar, the same penalty weight applies to all variables in the model. If a vector, it must have the same length as params, and contains a penalty weight for each coefficient.

  • L1_wt (scalar) – The fraction of the penalty given to the L1 penalty term. Must be between 0 and 1 (inclusive). If 0, the fit is a ridge fit, if 1 it is a lasso fit.

  • start_params (array-like) – Starting values for params.

  • profile_scale (bool) – If True the penalized fit is computed using the profile (concentrated) log-likelihood for the Gaussian model. Otherwise the fit uses the residual sum of squares.

  • refit (bool) – If True, the model is refit using only the variables that have non-zero coefficients in the regularized fit. The refitted model is not regularized.

  • distributed (bool) – If True, the model uses distributed methods for fitting, will raise an error if True and partitions is None.

  • generator (function) – generator used to partition the model, allows for handling of out of memory/parallel computing.

  • partitions (scalar) – The number of partitions desired for the distributed estimation.

  • threshold (scalar or array-like) – The threshold below which coefficients are zeroed out, only used for distributed estimation

Returns

Return type

A RegularizedResults instance.

Notes

The elastic net uses a combination of L1 and L2 penalties. The implementation closely follows the glmnet package in R.

The function that is minimized is:

\[0.5*RSS/n + alpha*((1-L1\_wt)*|params|_2^2/2 + L1\_wt*|params|_1)\]

where RSS is the usual regression sum of squares, n is the sample size, and \(|*|_1\) and \(|*|_2\) are the L1 and L2 norms.

For WLS and GLS, the RSS is calculated using the whitened endog and exog data.

Post-estimation results are based on the same data used to select variables, hence may be subject to overfitting biases.

The elastic_net method uses the following keyword arguments:

maxiterint

Maximum number of iterations

cnvrg_tolfloat

Convergence threshold for line searches

zero_tolfloat

Coefficients below this threshold are treated as zero.

The square root lasso approach is a variation of the Lasso that is largely self-tuning (the optimal tuning parameter does not depend on the standard deviation of the regression errors). If the errors are Gaussian, the tuning parameter can be taken to be

alpha = 1.1 * np.sqrt(n) * norm.ppf(1 - 0.05 / (2 * p))

where n is the sample size and p is the number of predictors.

The square root lasso uses the following keyword arguments:

zero_tolfloat

Coefficients below this threshold are treated as zero.

References

Friedman, Hastie, Tibshirani (2008). Regularization paths for generalized linear models via coordinate descent. Journal of Statistical Software 33(1), 1-22 Feb 2010.

A Belloni, V Chernozhukov, L Wang (2011). Square-root Lasso: pivotal recovery of sparse signals via conic programming. Biometrika 98(4), 791-806. https://arxiv.org/pdf/1009.5689.pdf

hessian(params, scale=None)

Evaluate the Hessian function at a given point.

Parameters

  • params (array-like) – The parameter vector at which the Hessian is computed.

  • scale (float or None) – If None, return the profile (concentrated) log likelihood (profiled over the scale parameter), else return the log-likelihood using the given scale value.

Returns

Return type

The Hessian matrix.

hessian_factor(params, scale=None, observed=True)

Weights for calculating Hessian

Parameters

  • params (ndarray) – parameter at which Hessian is evaluated

  • scale (None or float) – If scale is None, then the default scale will be calculated. Default scale is defined by self.scaletype and set in fit. If scale is not None, then it is used as a fixed scale.

  • observed (bool) – If True, then the observed Hessian is returned. If false then the expected information matrix is returned.

Returns

hessian_factor – A 1d weight vector used in the calculation of the Hessian. The hessian is obtained by (exog.T * hessian_factor).dot(exog)

Return type

ndarray, 1d

loglike(params, scale=None)

The likelihood function for the OLS model.

Parameters

  • params (array-like) – The coefficients with which to estimate the log-likelihood.

  • scale (float or None) – If None, return the profile (concentrated) log likelihood (profiled over the scale parameter), else return the log-likelihood using the given scale value.

Returns

Return type

The likelihood function evaluated at params.

score(params, scale=None)

Evaluate the score function at a given point.

The score corresponds to the profile (concentrated) log-likelihood in which the scale parameter has been profiled out.

Parameters

  • params (array-like) – The parameter vector at which the score function is computed.

  • scale (float or None) – If None, return the profile (concentrated) log likelihood (profiled over the scale parameter), else return the log-likelihood using the given scale value.

Returns

Return type

The score vector.

whiten(Y)

OLS model whitener does nothing: returns Y.

trtools.associaTR.main(args)
trtools.associaTR.perform_gwas(outfname, tr_vcf, phenotype_name, traits_fnames, vcftype, same_samples, sample_fname, region, non_major_cutoff, beagle_dosages, plotting_phenotype_fname, paired_genotype_plot, plot_phenotype_residuals, plotting_ci_alphas, imputed_ukb_strs_paper_period_check)
trtools.associaTR.perform_gwas_helper(outfile, all_samples, get_genotype_iter, phenotype_name, trait_fnames, same_samples, sample_fname, beagle_dosages, plotting_phenotype_fname, paired_genotype_plot, plot_phenotype_residuals, plotting_ci_alphas)
trtools.associaTR.run()