pseudovalidate: Function to perform pseudovalidation from a lassosum.pipeline...

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

Description

Function to perform pseudovalidation from a lassosum.pipeline object

Usage

pseudovalidate(...)

## S3 method for class 'lassosum.pipeline'
pseudovalidate(ls.pipeline,
  test.bfile = NULL, keep = NULL, remove = NULL, trace = 1,
  destandardize = F, plot = T, exclude.ambiguous = T,
  cluster = NULL, rematch = !is.null(test.bfile), ...)

Arguments

...	parameters to pass to pseudovalidation
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
trace	Controls amount of output
destandardize	Should coefficients from lassosum be destandardized using test dataset standard deviations before being returned?
plot	Should the validation plot be plotted?
exclude.ambiguous	Should ambiguous SNPs (C/G, A/T) be excluded?
cluster	A cluster object from the parallel package for parallel computing
rematch	Forces a rematching of the ls.pipline beta's with the new .bim file

Details

Pseudovalidation is explained in Mak et al (2016). It helps choosing a value of lambda and s in the absence of a validation phenotype.

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