pseudoAicBic: Function to obtain pseudo-AIC and pseudo-BIC estimates given...
In jpattee/penRegSum:

Description Usage Arguments Details

View source: R/pseudoAicBic.R

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

pseudoAicBic(
  penalizedBetas,
  betas,
  ses,
  N,
  refPanel,
  sigSqReg = 0.2,
  sseReg = 0.2,
  sigSqInd = NULL,
  allele1 = NULL,
  allele2 = NULL,
  standardized = TRUE,
  extract = NULL,
  ldBlocks = NULL
)

`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.

jpattee/penRegSum documentation built on Jan. 23, 2021, 12:59 a.m.