pgs: Computes polygenic scores as a genotype matrix multiplied by...
In tshmak/lassosum: LASSO with summary statistics and a reference panel

Description Usage Arguments Details Value Note

Note that this is a low-level command. For applying estimated betas to new bfiles, refer to https://github.com/tshmak/lassosum#apply-validated-betas-to-new-data

pgs(bfile, weights, ...)

.pgs(...)

## Default S3 method:
.pgs(weights, bfile, keep = NULL, extract = NULL,
  exclude = NULL, remove = NULL, chr = NULL, cluster = NULL,
  trace = 0, sparse = TRUE)

`bfile`	A plink bfile stem
`weights`	The weights for the SNPs (β)
`keep`	samples to keep (see `parseselect`)
`extract`	SNPs to extract (see `parseselect`)
`exclude`	SNPs to exclude (see `parseselect`)
`remove`	samples to remove (see `parseselect`)
`chr`	a vector of chromosomes
`cluster`	A `cluster` object from the `parallel` package. For parallel processing.
`trace`	Level of output
`sparse`	Assumes sparse weights matrix

A function to calculate Xβ where X is the genotype matrix in the plink bfile.

A matrix of Polygenic Scores

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 weights should be the same as the number of SNPs in the bfile after extract/exclude/chr.

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