pseudovalidation: Performs 'pseudovalidation' to select the best lambda value...
In tshmak/lassosum: LASSO with summary statistics and a reference panel

Performs ‘pseudovalidation’ to select the best λ value in lassosum

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pseudovalidation(bfile, beta, cor, sd = NULL, keep = NULL,
  extract = NULL, exclude = NULL, remove = NULL, chr = NULL,
  cluster = NULL, ...)

`bfile`	A plink bfile stem
`beta`	The matrix of estimated βs
`cor`	The vector of correlations (r)
`sd`	The standard deviation of the SNPs
`keep`	samples to keep
`extract`	SNPs to extract
`exclude`	SNPs to exclude
`remove`	samples to remove
`chr`	a vector of chromosomes
`cluster`	A `cluster` object from the `parallel` package for parallel computing

A function to calculate

f(λ)=β'r/√{β'X'Xβ}

where X is the standardized genotype matrix divided by √ n, and r is a vector of (shrunken) correlations.

the results of the pseudovalidation, i.e. f(λ)

Missing genotypes are interpreted as having the homozygous A2 alleles in the PLINK files (same as the --fill-missing-a2 option in PLINK).
The number of rows in beta and the length of cor should be the same as the number of SNPs in the bfile after extract/exclude/chr.