tlpSum: Function to obtain TLP effect size estimates given summary...

In jpattee/penRegSum:

Description

Function to obtain TLP effect size estimates given summary statistics and a reference panel

Usage

tlpSum(
  cors,
  bfile,
  lambdas,
  taus,
  s = 0.5,
  thr = 1e-04,
  init = NULL,
  maxIter = 1000,
  extract = NULL,
  ldBlocks = NULL,
  corBim = NULL
)

Arguments

cors	A vector of correlations, representing the univariate SNP-phenotype associations from the summary statistic data.
bfile	The stem of a PLINK binary file to be used as a reference panel.
lambdas	Vector of values of lambda.
taus	Vector of values of tau.
s	Vector of values for s.
thr	Convergence threshold.
init	Initial values for β.
maxIter	Maximum number of iterations.
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.
corBim	Optional PLINK formatted '.bim' file that specifies SNP labels and locations for 'cors' vector. If non-null, will check for SNPs missing in the reference panel and handle ensuing estimation.

Details

Function finds the minimum of the TLP objective function

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