Description Usage Arguments Details Value Note
This is to enable S3 parsing by the second argument
Computes polygenic scores as a genotype matrix multiplied by a matrix of weights
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
bfile |
A plink bfile stem |
weights |
The weights for the SNPs (β) |
keep |
samples to keep (see |
extract |
SNPs to extract (see |
exclude |
SNPs to exclude (see |
remove |
samples to remove (see |
chr |
a vector of chromosomes |
cluster |
A |
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.
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