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
1
ERROR
13
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Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | ERROR |
| 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 details (14 non-OK)
OK
r-devel-linux-x86_64-debian-clang
*
ERROR
r-devel-linux-x86_64-debian-gcc
tests
Running ‘testthat.R’ [121s/154s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat);
> library(ApplyPolygenicScore);
>
> test_check('ApplyPolygenicScore');
Input data passed validation
Input data passed validation
Saving _problems/test-pgs-statistics-371.R
Skipping test for >12 PGS columns as 'scales' package is available and will be used.
Saving _problems/test-pgs-statistics-559.R
Saving _problems/test-plotting-136.R
Saving _problems/test-plotting-431.R
Saving _problems/test-plotting-741.R
[1] "springgreen3"
[1] "darkturquoise"
[1] "springgreen3"
[1] "darkturquoise"
Saving _problems/test-plotting-995.R
[ FAIL 6 | WARN 87 | SKIP 0 | PASS 625 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-pgs-statistics.R:363:9'): analyze.pgs.binary.predictiveness validates binary phenotype columns ──
Error in `basename(x)`: a character vector argument expected
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-pgs-statistics.R:363:9
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─ApplyPolygenicScore::analyze.pgs.binary.predictiveness(...)
8. └─BoutrosLab.plotting.general::create.multipanelplot(...)
9. └─BoutrosLab.plotting.general:::get.legend.height(...)
10. └─tools::file_ext(filename)
11. ├─base::ifelse(...)
12. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x))
13. │ └─base::is.factor(x)
14. └─base::basename(x)
── Error ('test-pgs-statistics.R:552:9'): analyze.pgs.binary.predictiveness correctly formats outputs ──
Error in `basename(x)`: a character vector argument expected
Backtrace:
▆
1. └─ApplyPolygenicScore::analyze.pgs.binary.predictiveness(...) at test-pgs-statistics.R:552:9
2. └─BoutrosLab.plotting.general::create.multipanelplot(...)
3. └─BoutrosLab.plotting.general:::get.legend.height(...)
4. └─tools::file_ext(filename)
5. ├─base::ifelse(...)
6. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x))
7. │ └─base::is.factor(x)
8. └─base::basename(x)
── Error ('test-plotting.R:132:9'): create.pgs.density.plot runs with no error with basic inputs ──
Error in `basename(x)`: a character vector argument expected
Backtrace:
▆
1. └─ApplyPolygenicScore::create.pgs.density.plot(...) at test-plotting.R:132:9
2. └─BoutrosLab.plotting.general::create.multipanelplot(...)
3. └─BoutrosLab.plotting.general:::get.legend.height(...)
4. └─tools::file_ext(filename)
5. ├─base::ifelse(...)
6. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x))
7. │ └─base::is.factor(x)
8. └─base::basename(x)
── Error ('test-plotting.R:426:9'): create.pgs.with.continuous.phenotype.plot runs with no error with basic inputs ──
Error in `basename(x)`: a character vector argument expected
Backtrace:
▆
1. └─ApplyPolygenicScore::create.pgs.with.continuous.phenotype.plot(...) at test-plotting.R:426:9
2. └─BoutrosLab.plotting.general::create.multipanelplot(...)
3. └─BoutrosLab.plotting.general:::get.legend.height(...)
4. └─tools::file_ext(filename)
5. ├─base::ifelse(...)
6. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x))
7. │ └─base::is.factor(x)
8. └─base::basename(x)
── Error ('test-plotting.R:737:9'): create.pgs.rank.plot runs with no error with basic inputs ──
Error in `basename(x)`: a character vector argument expected
Backtrace:
▆
1. └─ApplyPolygenicScore::create.pgs.rank.plot(...) at test-plotting.R:737:9
2. └─BoutrosLab.plotting.general::create.multipanelplot(...)
3. └─BoutrosLab.plotting.general:::get.legend.height(...)
4. └─tools::file_ext(filename)
5. ├─base::ifelse(...)
6. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x))
7. │ └─base::is.factor(x)
8. └─base::basename(x)
── Error ('test-plotting.R:991:9'): create.pgs.boxplot runs with no error with basic inputs ──
Error in `basename(x)`: a character vector argument expected
Backtrace:
▆
1. └─ApplyPolygenicScore::create.pgs.boxplot(...) at test-plotting.R:991:9
2. └─BoutrosLab.plotting.general::create.multipanelplot(...)
3. └─BoutrosLab.plotting.general:::get.legend.height(...)
4. └─tools::file_ext(filename)
5. ├─base::ifelse(...)
6. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x))
7. │ └─base::is.factor(x)
8. └─base::basename(x)
[ FAIL 6 | WARN 87 | SKIP 0 | PASS 625 ]
Error:
! Test failures.
Execution halted
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
*
Check History
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 9, 2026
ERROR
r-devel-linux-x86_64-debian-gcc
tests
Running ‘testthat.R’ [121s/154s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat);
> library(ApplyPolygenicScore);
>
> test_check('ApplyPolygenicScore');
Input data passed validation
Input data passed validation
Saving _problems/test-pgs-statistics-371.R
Skipping test for >12 PGS columns as 'scales' package is available and will be used.
Saving _problems/test-pgs-statistics-559.R
Saving _problems/test-plotting-136.R
Saving _problems/te
Dependency Network
Version History
new
4.0.2
Mar 9, 2026