validate: Function to validate output from lassosum.pipeline with...
In tshmak/lassosum: LASSO with summary statistics and a reference panel

Function to validate output from lassosum.pipeline with external phenotype

validate(...)

## S3 method for class 'lassosum.pipeline'
validate(ls.pipeline, test.bfile = NULL,
  keep = NULL, remove = NULL, pheno = NULL, covar = NULL,
  validate.function = function(x, y) cor(x, y, use = "complete"),
  trace = 1, destandardize = F, plot = T, exclude.ambiguous = T,
  cluster = NULL, rematch = !is.null(test.bfile), ...)

`...`	parameters to pass to `sd.bfile`
`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
`validate.function`	Function with which to perform validation
`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

Chooses the best lambda and s by validating polygenic score against an external phenotype in the testing dataset. If pheno is not specified, then the sixth column in the testing dataset .fam.fam file is used.

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