Description Usage Arguments Details

Function to obtain pseudo-AIC and pseudo-BIC estimates given summary statistics and a reference panel

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`penalizedBetas` |
Polygenic risk score effect size estimates. These are the estimates for which we want to approximate AIC and BIC. May be a matrix. |

`betas` |
Univariate effect size estimates. |

`ses` |
Standard errors of the univariate effect size estimates. |

`N` |
Sample sizes corresponding to the univariate effect size estimates. Can be a constant or a vector. |

`refPanel` |
Stem of PLINK binary file |

`sigSqReg` |
The matrix regularization parameter for the estimation of the residual variance. Default is .2. |

`sseReg` |
The matrix regularization parameter for the estimation of the SSE. Default is .2. |

`sigSqInd` |
Index of SNPs to be used for estimation of residual variance. If null, default is to pick the n/5 SNPs with largest univariate effect sizes, where n is the sample size of the reference panel. |

`allele1` |
Vector of effect alleles for the betas and penalizedBetas. Corresponds to the fifth column of a PLINK .bim file. |

`allele2` |
Vector of reference alleles for the betas and penalizedBetas. Corresponds to the sixth column of a PLINK .bim file. |

`standardized` |
Set to true if the coefficient estimates for penalizedBetas are standardized. Note that elastSum and tlpSum output standardized estimates. |

`extract` |
Vector of the indices of SNPs to keep. If null, will keep all SNPs. |

`ldBlocks` |
Location of file specifying independent LD Blocks to be used. File should be in the BED file format. If null, estimation is done by chromosome. |

Function requires univariate effect size estimates, standard errors, and sample sizes, candidate polygenic risk score estimates, and a reference panel.

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