API for ApplyPolygenicScore
Utilities for the Application of a Polygenic Score to a VCF

Global functions
add.slop Source code
apply.polygenic.score Man page Source code
assemble.heatmap.colors Source code
assess.pgs.vcf.allele.match Man page Source code
calculate.missing.genotype.dosage Source code
check.for.no.info.fields Source code
check.pgs.weight.columns Man page Source code
check.vcf.for.split.multiallelic.sites Source code
classify.variable.type Source code
combine.pgs.bed Man page Source code
combine.vcf.with.pgs Man page Source code
convert.allele.frequency.to.dosage Man page Source code
convert.alleles.to.pgs.dosage Man page Source code
convert.pgs.to.bed Man page Source code
create.feature.color.vector Source code
create.pgs.density.plot Man page Source code
create.pgs.rank.plot Man page Source code
create.pgs.with.continuous.phenotype.plot Man page Source code
custom.aggregation.function Source code
flip.DNA.allele Man page Source code
format.chromosome.notation Man page Source code
generate.filename Source code
get.combined.multiallelic.variant.by.sample.matrix Source code
get.na.coordinates.for.heatmap Source code
get.non.risk.multiallelic.site.row Source code
get.pgs.percentiles Man page Source code
get.variant.by.sample.matrix Source code
import.pgs.weight.file Man page Source code
import.vcf Man page Source code
open.input.connection Source code
parse.pgs.input.header Man page Source code
pgs.distribution.plotting.input.checks Source code
rank.plotting.input.checks Source code
run.pgs.regression Man page Source code
split.pgs.by.phenotype Source code
validate.allele.input Source code
validate.file.write.inputs Source code
validate.pgs.data.input Source code
validate.phenotype.data.input Source code
validate.vcf.input Source code
write.apply.polygenic.score.output.to.file Man page Source code
write.per.sample.pgs.table Source code
write.pgs.regression.table Source code
ApplyPolygenicScore documentation built on April 4, 2025, 12:18 a.m.