pgs: Computes polygenic scores as a genotype matrix multiplied by...

In SeojinHwang/scadsum: nonconvex penalty with summary statistics and a reference panel

Computes polygenic scores as a genotype matrix multiplied by a matrix of weights

Description

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

Usage

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
)

Arguments

bfile	A plink bfile stem
weights	The weights for the SNPs (\beta)
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

Details

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

Value

A matrix of Polygenic Scores

Note

• 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.

SeojinHwang/scadsum documentation built on June 30, 2023, 10:52 p.m.