validate: Validate the performance of EBPRS

In EBPRS: Derive Polygenic Risk Score Based on Emprical Bayes Theory

Description

Provide the performance evaluated by predictive r2 and AUC.

Usage

validate(score, truey)

Arguments

score	polygenic score generated by 'EBPRS'
truey	the true phenotype (the 6th column in the fam file)

Author(s)

Shuang Song, Wei Jiang, Lin Hou and Hongyu Zhao

References

Song S, Jiang W, Hou L, Zhao H (2020) Leveraging effect size distributions to improve polygenic risk scores derived from summary statistics of genome-wide association studies. PLoS Comput Biol 16(2): e1007565. https://doi.org/10.1371/journal.pcbi.1007565

See Also

EBPRS

Examples

validate(score=rnorm(20,0,1), truey=sample(0:1,20,replace=TRUE))

Example output

Loading required package: ROCR
Loading required package: BEDMatrix
Loading required package: data.table
The R2 equals to  0.01361416 
The AUC equals to 0.5625 
$r2
[1] 0.01361416

$AUC
[1] 0.5625

EBPRS documentation built on Aug. 26, 2020, 9:06 a.m.