PRSPGx (version 0.3.0)

PRS_PGx_CT: Construct PGx PRS unadjusted or using clumping and thresholding

Description

Shrink prognostic and predictive effect sizes simutaneously by 2-df (main and interaction) p-value cutoff (PRS-PGx-CT turns out to be PRS-PGx-Unadj when setting p-value cutoff = 1)

Usage

PRS_PGx_CT(
  PGx_GWAS,
  G_reference,
  pcutoff = 1e-04,
  clumping = TRUE,
  p1 = 1e-04,
  d1 = 250000,
  r1 = 0.8
)

Value

A numeric list, the first sublist contains estimated prognostic effect sizes, the second sublist contains estimated predictive effect sizes, the third sublist contains 2-df p-values

Arguments

PGx_GWAS

a numeric matrix containing PGx GWAS summary statistics, including SNP ID, MAF, position, \(\beta\), \(\alpha\), 2-df p-value, and N

G_reference

a numeric matrix containing the individual-level genotype information from the reference panel (e.g., 1KG)

pcutoff

a numeric value indicating the p-value cutoff

clumping

a logical flag indicating should clumping be performed

p1

a numeric value indicating p-value threshold to decide flag SNPs in clumping

d1

a numeric value indicating window size in clumping

r1

a numeric value indicating correlation in clumping

Author

Song Zhai

Details

PRS-PGx-CT only needs PGx summary statistics

References

Zhai, S., Zhang, H., Mehrotra, D.V. & Shen, J. Paradigm Shift from Disease PRS to PGx PRS for Drug Response Prediction using PRS-PGx Methods (submitted).

Examples

data(PRSPGx.example); attach(PRSPGx.example)
coef_est <- PRS_PGx_CT(PGx_GWAS, G_reference, pcutoff = 0.01, clumping = TRUE)
summary(coef_est$coef.G)
summary(coef_est$coef.TG)