# Utilities for the Application of a Polygenic Score to a VCF

## Documentation for package ‘ApplyPolygenicScore’ version 4.0.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

analyze.pgs.binary.predictiveness | Analyze PGS Predictiveness for Binary Phenotypes
apply.polygenic.score | Apply polygenic score to VCF data
assess.pgs.vcf.allele.match | Assess PGS allele match to VCF allele
check.pgs.weight.columns | Check PGS weight file columns
combine.pgs.bed | Combine PGS BED files
combine.vcf.with.pgs | Combine VCF with PGS
convert.allele.frequency.to.dosage | Convert allele frequency to mean dosage
convert.alleles.to.pgs.dosage | Convert alleles to dosage
convert.pgs.to.bed | Convert PGS data to BED format
create.pgs.boxplot | Plot PGS Boxplots
create.pgs.density.plot | Plot PGS Density
create.pgs.rank.plot | Plot PGS Rank
create.pgs.with.continuous.phenotype.plot | Plot PGS Scatterplots
flip.DNA.allele | Flip DNA allele
format.chromosome.notation | Format chromosome names
get.pgs.percentiles | get.pgs.percentiles
import.pgs.weight.file | Import PGS weight file
import.vcf | Import VCF file
parse.pgs.input.header | Parse PGS input file header
run.pgs.regression | Run linear and logistic regression on a polygenic score and a set of phenotypes
write.apply.polygenic.score.output.to.file | Write apply.polygenic.score output to file