subset.ssCTPR.pipeline: Subset a ssCTPR.pipeline object by lambda, s and lambda_ct

In yingxi-kaylee/ssCTPR: Cross-Trait Penalized Regression using Summary Statistics

Description

Subset a ssCTPR.pipeline object by lambda, s and lambda_ct

Usage

## S3 method for class 'ssCTPR.pipeline'
subset(ssCTPR.pipeline, s = NULL, lambda = NULL, lambda_ct = NULL)

Arguments

ssCTPR.pipeline	An object returned by ssCTPR.pipeline
s	Value(s) of s to restrict to
lambda	Value(s) of lambda to restrict to
lambda_ct	Values(s) of lambda_ct to restrict to

Details

This function is usually used to reapply a validated pgs to a new data.set. See example below.

Value

A ssCTPR.pipeline object

Examples

## Not run: 
 ### Run ssCTPR using standard pipeline ### 
 lp <- ssCTPR.pipeline(cor=cor, traits=ncol(cor), lambda_ct = lambda_ct,
                          chr=ss$Chr, pos=ss$Position, 
                          A1=ss$A1, A2=ss$A2,
                          ref.bfile=ref.bfile, test.bfile=test.bfile, 
                          LDblocks = ld)
 v <- validate(lp)
 lp2 <- subset(lp, s=v$best.s, lambda=v$best.lambda, lambda_ct=v$best.lambda_ct)
 v2 <- validate(lp2)

## End(Not run)

yingxi-kaylee/ssCTPR documentation built on Nov. 14, 2021, 5:24 a.m.