Package: ApplyPolygenicScore 3.0.1
ApplyPolygenicScore: Utilities for the Application of a Polygenic Score to a VCF
Simple and transparent parsing of genotype/dosage data from an input Variant Call Format (VCF) file, matching of genotype coordinates to the component Single Nucleotide Polymorphisms (SNPs) of an existing polygenic score (PGS), and application of SNP weights to dosages for the calculation of a polygenic score for each individual in accordance with the additive weighted sum of dosages model. Methods are designed in reference to best practices described by Collister, Liu, and Clifton (2022) <doi:10.3389/fgene.2022.818574>.
Authors:
ApplyPolygenicScore_3.0.1.tar.gz
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ApplyPolygenicScore.pdf |ApplyPolygenicScore.html✨
ApplyPolygenicScore/json (API)
NEWS
| # Install 'ApplyPolygenicScore' in R: |
| install.packages('ApplyPolygenicScore', repos = c('https://pboutros.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 8 days agofrom:af9179b56e. Checks:9 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 06 2025 |
| R-4.5-win | OK | Mar 06 2025 |
| R-4.5-mac | OK | Mar 06 2025 |
| R-4.5-linux | OK | Mar 06 2025 |
| R-4.4-win | OK | Mar 06 2025 |
| R-4.4-mac | OK | Mar 06 2025 |
| R-4.4-linux | OK | Mar 06 2025 |
| R-4.3-win | OK | Mar 06 2025 |
| R-4.3-mac | OK | Mar 06 2025 |
Exports:apply.polygenic.scoreassess.pgs.vcf.allele.matchcombine.pgs.bedcombine.vcf.with.pgsconvert.allele.frequency.to.dosageconvert.alleles.to.pgs.dosageconvert.pgs.to.bedcreate.pgs.density.plotcreate.pgs.rank.plotcreate.pgs.with.continuous.phenotype.plotflip.DNA.alleleformat.chromosome.notationget.pgs.percentilesimport.pgs.weight.fileimport.vcfparse.pgs.input.headerrun.pgs.regression
Dependencies:apeBoutrosLab.plotting.generalclasscliclusterdata.tabledeldirdigestdplyre1071fansigenericsgluegridExtragtablehexbininterpjpeglatticelatticeExtralifecyclemagrittrMASSMatrixmemusemgcvnlmepermutepillarpinfsc50pkgconfigplyrpngpROCproxyR6RColorBrewerRcppRcppEigenreshape2rlangstringistringrtibbletidyselectutf8vcfRvctrsveganviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Apply polygenic score to VCF data | apply.polygenic.score |
| Assess PGS allele match to VCF allele | assess.pgs.vcf.allele.match |
| Check PGS weight file columns | check.pgs.weight.columns |
| Combine PGS BED files | combine.pgs.bed |
| Combine VCF with PGS | combine.vcf.with.pgs |
| Convert allele frequency to mean dosage | convert.allele.frequency.to.dosage |
| Convert alleles to dosage | convert.alleles.to.pgs.dosage |
| Convert PGS data to BED format | convert.pgs.to.bed |
| Plot PGS Density | create.pgs.density.plot |
| Plot PGS Rank | create.pgs.rank.plot |
| Plot PGS Scatterplots | create.pgs.with.continuous.phenotype.plot |
| Flip DNA allele | flip.DNA.allele |
| Format chromosome names | format.chromosome.notation |
| get.pgs.percentiles | get.pgs.percentiles |
| Import PGS weight file | import.pgs.weight.file |
| Import VCF file | import.vcf |
| Parse PGS input file header | parse.pgs.input.header |
| Run linear and logistic regression on a polygenic score and a set of phenotypes | run.pgs.regression |
| Write apply.polygenic.score output to file | write.apply.polygenic.score.output.to.file |
