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

Description Usage Arguments Details

View source: R/tlpSum.R

Description

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

Usage

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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.