quasicors: Function to obtain quasi-correlation estimates given
In jpattee/penRegSum:

Description Usage Arguments Details

View source: R/quasicors.R

Function to obtain quasi-correlation estimates given

quasicors(
  testBetas,
  testSes,
  N,
  penalizedBetas,
  refPanel,
  allele1 = NULL,
  allele2 = NULL,
  standardized = TRUE,
  trainVar = NULL,
  allele1.test = NULL,
  allele2.test = NULL
)

`testBetas`	Univariate effect sizes for the out-of-sample data
`testSes`	Univariate standard errors for the effect sizes of the out-of-sample data
`N`	Sample sizes corresponding to the testBetas. Can be a constant or a vector.
`penalizedBetas`	The polygenic risk scores to be tested on the out-of-sample data. May be a matrix.
`refPanel`	PLINK stem for binary file to be used as the reference panel
`allele1`	Vector of effect alleles for the penalizedBetas. Corresponds to the fifth column of a PLINK .bim file.
`allele2`	Vector of reference alleles for the 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.
`trainVar`	Phenotypic variance for data used to estimate the penalizedBetas. Only necessary if standardized = TRUE
`allele1.test`	Vector of effect alleles for the testBetas. Corresponds to the fifth column of a PLINK .bim file.
`allele2.test`	Vector of reference alleles for the testBetas. Corresponds to the sixth column of a PLINK .bim file.
`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.