Utilities for the Application of a Polygenic Score to a VCF


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Documentation for package ‘ApplyPolygenicScore’ version 3.0.1

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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.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