splitvalidate: Function to perform split-validation using output from...

In tshmak/lassosum: LASSO with summary statistics and a reference panel

Description

Function to perform split-validation using output from lassosum.pipeline with external phenotype

Usage

splitvalidate(...)

## S3 method for class 'lassosum.pipeline'
splitvalidate(ls.pipeline, test.bfile = NULL,
  keep = NULL, remove = NULL, pheno = NULL, covar = NULL,
  trace = 1, split = NULL, rematch = !is.null(test.bfile), ...)

Arguments

...	parameters to pass to validate.lassosum.pipeline
ls.pipeline	A lassosum.pipeline object
test.bfile	The (PLINK bfile for the test dataset
keep	Participants to keep (see lassosum for more details)
remove	Participants to remove
pheno	A vector of phenotype OR a data.frame with 3 columns, the first 2 columns being headed "FID" and "IID", OR a filename for such a data.frame
covar	A matrix of covariates OR a data.frame with 3 or more columns, the first 2 columns being headed "FID" and "IID", OR a filename for such a data.frame
trace	Controls amount of output
rematch	Forces a rematching of the ls.pipline beta's with the new .bim file

Details

Performs split-validation. Randomly split the test data into half for validation and half for prediction. Standardize the best cross-predicted pgs and stack together.

tshmak/lassosum documentation built on Sept. 24, 2020, 9:41 a.m.