API for ApplyPolygenicScore
Utilities for the Application of a Polygenic Score to a VCF
| Global functions | |
|---|---|
| FUN | Source code Source code Source code |
| add.slop | Source code |
| analyze.pgs.binary.predictiveness | Man page |
| 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.long.vcf.to.wide.vcf | Source code |
| convert.pgs.to.bed | Man page Source code |
| create.feature.color.vector | Source code |
| create.pgs.boxplot | Man page 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.mean.dosage.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 |
