ApplyPolygenicScore
Utilities for the Application of a Polygenic Score to a VCF
v4.0.2
·
Feb 26, 2026
·
GPL-2
Description
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>.
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CRAN Check Status
14
OK
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 11, 2026
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 10, 2026
ERROR
r-devel-windows-x86_64
tests
Running 'testthat.R' [163s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat);
> library(ApplyPolygenicScore);
>
> test_check('ApplyPolygenicScore');
Input data passed validation
Input data passed valid
...[truncated]...
ifelse(...)
6. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x))
7. │ └─base::is.factor(x)
8. └─base::basename(x)
[ FAIL 6 | WARN 87 | SKIP 0 | PASS 625 ]
Error:
! Test failures.
Execution halted